PDB Short entry for 5KIT HEADER TRANSFERASE/TRANSFERASE INHIBITOR 17-JUN-16 5KIT TITLE CRYSTAL STRUCTURE OF NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE (NAMPT) IN TITLE 2 COMPLEX WITH INHIBITORS 37 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NAMPT,PRE-B-CELL COLONY-ENHANCING FACTOR 1,PRE-B CELL- COMPND 5 ENHANCING FACTOR,VISFATIN; COMPND 6 EC: 2.4.2.12; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NAMPT, PBEF, PBEF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.LI,W.WANG REVDAT 3 06-MAR-24 5KIT 1 JRNL REMARK REVDAT 2 05-OCT-16 5KIT 1 JRNL REVDAT 1 31-AUG-16 5KIT 0 JRNL AUTH M.ZAK,P.W.YUEN,X.LIU,S.PATEL,D.SAMPATH,J.OEH,B.M.LIEDERER, JRNL AUTH 2 W.WANG,T.O'BRIEN,Y.XIAO,N.SKELTON,R.HUA,J.SODHI,Y.WANG, JRNL AUTH 3 L.ZHANG,G.ZHAO,X.ZHENG,Y.C.HO,K.W.BAIR,P.S.DRAGOVICH JRNL TITL MINIMIZING CYP2C9 INHIBITION OF EXPOSED-PYRIDINE NAMPT JRNL TITL 2 (NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE) INHIBITORS. JRNL REF J.MED.CHEM. V. 59 8345 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27541271 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00697 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 131229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 6609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.9568 - 4.9675 0.96 4352 199 0.1612 0.1626 REMARK 3 2 4.9675 - 3.9440 0.97 4321 226 0.1253 0.1432 REMARK 3 3 3.9440 - 3.4458 0.98 4318 226 0.1386 0.1591 REMARK 3 4 3.4458 - 3.1308 0.99 4349 225 0.1432 0.1815 REMARK 3 5 3.1308 - 2.9065 0.99 4389 229 0.1372 0.1811 REMARK 3 6 2.9065 - 2.7352 0.99 4350 240 0.1357 0.1710 REMARK 3 7 2.7352 - 2.5982 1.00 4378 236 0.1247 0.1720 REMARK 3 8 2.5982 - 2.4852 1.00 4389 198 0.1226 0.1721 REMARK 3 9 2.4852 - 2.3895 1.00 4379 254 0.1207 0.1721 REMARK 3 10 2.3895 - 2.3071 1.00 4315 256 0.1168 0.1641 REMARK 3 11 2.3071 - 2.2349 0.99 4363 231 0.1259 0.1802 REMARK 3 12 2.2349 - 2.1710 1.00 4349 241 0.1262 0.1792 REMARK 3 13 2.1710 - 2.1139 1.00 4382 236 0.1228 0.1768 REMARK 3 14 2.1139 - 2.0623 1.00 4393 235 0.1285 0.1751 REMARK 3 15 2.0623 - 2.0154 1.00 4353 223 0.1188 0.1724 REMARK 3 16 2.0154 - 1.9725 1.00 4405 223 0.1095 0.1531 REMARK 3 17 1.9725 - 1.9331 1.00 4368 247 0.1032 0.1829 REMARK 3 18 1.9331 - 1.8966 1.00 4350 228 0.1170 0.1911 REMARK 3 19 1.8966 - 1.8627 1.00 4377 258 0.1182 0.1840 REMARK 3 20 1.8627 - 1.8312 1.00 4356 241 0.1211 0.2002 REMARK 3 21 1.8312 - 1.8016 1.00 4380 238 0.1343 0.1941 REMARK 3 22 1.8016 - 1.7739 1.00 4363 233 0.1364 0.1937 REMARK 3 23 1.7739 - 1.7478 0.99 4367 221 0.1477 0.2135 REMARK 3 24 1.7478 - 1.7232 0.94 4128 215 0.1693 0.2462 REMARK 3 25 1.7232 - 1.6999 0.89 3881 209 0.1944 0.2795 REMARK 3 26 1.6999 - 1.6778 0.85 3742 183 0.2051 0.2564 REMARK 3 27 1.6778 - 1.6569 0.80 3498 188 0.2110 0.2653 REMARK 3 28 1.6569 - 1.6369 0.75 3261 164 0.2295 0.3181 REMARK 3 29 1.6369 - 1.6179 0.70 3109 153 0.2536 0.3213 REMARK 3 30 1.6179 - 1.5997 0.61 2655 153 0.2644 0.3302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 39.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.19590 REMARK 3 B22 (A**2) : 0.07150 REMARK 3 B33 (A**2) : -3.26580 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.73450 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 7817 REMARK 3 ANGLE : 1.024 10584 REMARK 3 CHIRALITY : 0.073 1150 REMARK 3 PLANARITY : 0.005 1336 REMARK 3 DIHEDRAL : 13.034 2865 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 92 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 138334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2UL + 0.2UL DROPS CONTAINING 6MG/ML REMARK 280 NAMPT, 0.1M SODIUM PHOSPHATE, 25-29% POLYETHYLENE GLYCOL 3350, REMARK 280 0.2M NACL, 1MM COMPOUND, PH 8.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 53.29450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 43 REMARK 465 THR A 44 REMARK 465 GLU A 45 REMARK 465 ASN A 46 REMARK 465 SER A 47 REMARK 465 LYS A 48 REMARK 465 LEU A 49 REMARK 465 ARG A 50 REMARK 465 LYS A 51 REMARK 465 VAL A 52 REMARK 465 ALA A 488 REMARK 465 ALA A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 ALA B 4 REMARK 465 ALA B 5 REMARK 465 GLU B 6 REMARK 465 ALA B 7 REMARK 465 LYS B 43 REMARK 465 THR B 44 REMARK 465 GLU B 45 REMARK 465 ASN B 46 REMARK 465 SER B 47 REMARK 465 LYS B 48 REMARK 465 LEU B 49 REMARK 465 ARG B 50 REMARK 465 LYS B 51 REMARK 465 VAL B 52 REMARK 465 ALA B 488 REMARK 465 ALA B 489 REMARK 465 HIS B 490 REMARK 465 HIS B 491 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3 PO4 A 508 O HOH A 601 2.09 REMARK 500 OG1 THR B 391 OD1 ASP B 393 2.10 REMARK 500 OE2 GLU B 187 O HOH B 601 2.15 REMARK 500 O HOH B 619 O HOH B 630 2.16 REMARK 500 O HOH B 940 O HOH B 1065 2.17 REMARK 500 O LYS B 255 O HOH B 602 2.18 REMARK 500 O HOH A 660 O HOH A 1016 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 54 74.71 -107.73 REMARK 500 PHE A 96 125.46 175.82 REMARK 500 TYR A 231 -58.10 -127.09 REMARK 500 PHE A 269 59.09 -116.37 REMARK 500 GLU A 293 -67.06 -134.04 REMARK 500 ALA A 306 56.51 -140.82 REMARK 500 ASP A 313 22.05 -151.67 REMARK 500 ASP A 416 72.66 -158.34 REMARK 500 ASP B 94 43.51 -100.70 REMARK 500 TYR B 231 -59.27 -128.12 REMARK 500 PHE B 269 59.99 -117.36 REMARK 500 GLU B 293 -66.87 -130.43 REMARK 500 ASP B 313 21.39 -153.01 REMARK 500 ASP B 416 71.22 -159.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B1175 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B1176 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH B1177 DISTANCE = 6.77 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6TA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6TA B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 509 DBREF 5KIT A 1 491 UNP P43490 NAMPT_HUMAN 1 491 DBREF 5KIT B 1 491 UNP P43490 NAMPT_HUMAN 1 491 SEQRES 1 A 491 MET ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 A 491 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 A 491 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 A 491 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 A 491 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 A 491 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 A 491 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 A 491 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 A 491 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 A 491 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 A 491 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 A 491 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 A 491 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 A 491 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 A 491 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 A 491 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 A 491 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 A 491 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 A 491 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 A 491 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 A 491 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 A 491 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 A 491 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 A 491 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 A 491 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 A 491 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 A 491 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 A 491 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 A 491 VAL GLU GLY MET LYS GLN LYS MET TRP SER ILE GLU ASN SEQRES 30 A 491 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 A 491 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 A 491 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 A 491 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 A 491 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 A 491 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 A 491 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 A 491 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 A 491 LEU ASN ILE GLU LEU GLU ALA ALA HIS HIS SEQRES 1 B 491 MET ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 B 491 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 B 491 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 B 491 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 B 491 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 B 491 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 B 491 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 B 491 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 B 491 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 B 491 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 B 491 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 B 491 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 B 491 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 B 491 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 B 491 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 B 491 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 B 491 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 B 491 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 B 491 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 B 491 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 B 491 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 B 491 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 B 491 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 B 491 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 B 491 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 B 491 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 B 491 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 B 491 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 B 491 VAL GLU GLY MET LYS GLN LYS MET TRP SER ILE GLU ASN SEQRES 30 B 491 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 B 491 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 B 491 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 B 491 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 B 491 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 B 491 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 B 491 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 B 491 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 B 491 LEU ASN ILE GLU LEU GLU ALA ALA HIS HIS HET 6TA A 501 28 HET PO4 A 502 5 HET PO4 A 503 5 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET PO4 A 508 5 HET 6TA B 501 28 HET PO4 B 502 5 HET PO4 B 503 5 HET EDO B 504 4 HET EDO B 505 4 HET EDO B 506 4 HET EDO B 507 4 HET PO4 B 508 5 HET EDO B 509 4 HETNAM 6TA ~{TERT}-BUTYL (2~{S})-2-[(1,3-DIHYDROPYRROLO[3,4- HETNAM 2 6TA C]PYRIDIN-2-YLCARBONYLAMINO)METHYL]-6- HETNAM 3 6TA AZASPIRO[2.5]OCTANE-6-CARBOXYLATE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 6TA 2(C21 H30 N4 O3) FORMUL 4 PO4 6(O4 P 3-) FORMUL 6 EDO 9(C2 H6 O2) FORMUL 20 HOH *1182(H2 O) HELIX 1 AA1 ASN A 10 ALA A 14 5 5 HELIX 2 AA2 ASP A 16 GLN A 25 5 10 HELIX 3 AA3 GLY A 61 LEU A 70 1 10 HELIX 4 AA4 THR A 76 GLN A 92 1 17 HELIX 5 AA5 ASN A 97 ASP A 109 1 13 HELIX 6 AA6 ASP A 138 TYR A 142 5 5 HELIX 7 AA7 TRP A 143 ILE A 148 1 6 HELIX 8 AA8 ILE A 148 GLN A 154 1 7 HELIX 9 AA9 SER A 155 GLY A 181 1 27 HELIX 10 AB1 GLY A 185 TYR A 188 5 4 HELIX 11 AB2 GLY A 194 VAL A 198 5 5 HELIX 12 AB3 SER A 200 LEU A 212 1 13 HELIX 13 AB4 VAL A 221 TYR A 231 1 11 HELIX 14 AB5 GLU A 246 ALA A 252 1 7 HELIX 15 AB6 TRP A 253 ASP A 256 5 4 HELIX 16 AB7 HIS A 257 PHE A 269 1 13 HELIX 17 AB8 ASP A 282 LYS A 289 1 8 HELIX 18 AB9 LEU A 295 VAL A 300 1 6 HELIX 19 AC1 ASN A 316 PHE A 332 1 17 HELIX 20 AC2 ASP A 357 LYS A 371 1 15 HELIX 21 AC3 SER A 374 GLU A 376 5 3 HELIX 22 AC4 GLY A 383 GLN A 388 1 6 HELIX 23 AC5 ASP A 420 ARG A 424 5 5 HELIX 24 AC6 GLY A 446 GLU A 451 5 6 HELIX 25 AC7 SER A 472 ALA A 480 1 9 HELIX 26 AC8 ASN B 10 ALA B 14 5 5 HELIX 27 AC9 ASP B 16 GLN B 25 5 10 HELIX 28 AD1 GLY B 61 LEU B 70 1 10 HELIX 29 AD2 THR B 76 GLN B 92 1 17 HELIX 30 AD3 ASN B 97 ASP B 109 1 13 HELIX 31 AD4 ASP B 138 TYR B 142 5 5 HELIX 32 AD5 TRP B 143 ILE B 148 1 6 HELIX 33 AD6 ILE B 148 GLN B 154 1 7 HELIX 34 AD7 SER B 155 GLY B 181 1 27 HELIX 35 AD8 GLY B 185 TYR B 188 5 4 HELIX 36 AD9 GLY B 194 VAL B 198 5 5 HELIX 37 AE1 SER B 200 LEU B 212 1 13 HELIX 38 AE2 VAL B 221 TYR B 231 1 11 HELIX 39 AE3 GLU B 246 ALA B 252 1 7 HELIX 40 AE4 TRP B 253 ASP B 256 5 4 HELIX 41 AE5 HIS B 257 PHE B 269 1 13 HELIX 42 AE6 ASP B 282 LYS B 289 1 8 HELIX 43 AE7 LEU B 295 VAL B 300 1 6 HELIX 44 AE8 ASN B 316 PHE B 332 1 17 HELIX 45 AE9 ASP B 357 LYS B 371 1 15 HELIX 46 AF1 SER B 374 GLU B 376 5 3 HELIX 47 AF2 GLY B 383 GLN B 388 1 6 HELIX 48 AF3 ASP B 420 ARG B 424 5 5 HELIX 49 AF4 GLY B 446 GLU B 451 5 6 HELIX 50 AF5 SER B 472 ALA B 480 1 9 HELIX 51 AF6 LEU B 482 GLU B 487 1 6 SHEET 1 AA1 7 LEU A 409 ASN A 412 0 SHEET 2 AA1 7 CYS A 397 THR A 406 -1 N VAL A 404 O ILE A 411 SHEET 3 AA1 7 THR A 30 CYS A 39 -1 N TYR A 36 O LYS A 400 SHEET 4 AA1 7 VAL A 130 ASN A 136 -1 O VAL A 134 N SER A 35 SHEET 5 AA1 7 ILE A 114 ALA A 118 -1 N GLU A 115 O GLU A 135 SHEET 6 AA1 7 HIS A 459 LYS A 463 -1 O HIS A 459 N ALA A 118 SHEET 7 AA1 7 LYS A 466 VAL A 467 -1 O LYS A 466 N LYS A 463 SHEET 1 AA2 2 GLU A 56 VAL A 58 0 SHEET 2 AA2 2 VAL A 124 PRO A 126 -1 O ILE A 125 N THR A 57 SHEET 1 AA3 5 LEU A 190 ASP A 192 0 SHEET 2 AA3 5 ILE A 378 SER A 382 1 O PHE A 380 N HIS A 191 SHEET 3 AA3 5 LEU A 348 GLN A 352 1 N GLN A 352 O ALA A 379 SHEET 4 AA3 5 LEU A 308 ARG A 311 1 N ILE A 310 O ARG A 349 SHEET 5 AA3 5 VAL A 274 VAL A 277 1 N VAL A 274 O ILE A 309 SHEET 1 AA4 2 THR A 335 GLU A 336 0 SHEET 2 AA4 2 LYS A 342 LEU A 343 -1 O LEU A 343 N THR A 335 SHEET 1 AA5 2 SER A 431 ARG A 434 0 SHEET 2 AA5 2 PHE A 440 LEU A 443 -1 O VAL A 441 N HIS A 433 SHEET 1 AA6 7 LEU B 409 ASN B 412 0 SHEET 2 AA6 7 CYS B 397 THR B 406 -1 N VAL B 404 O ILE B 411 SHEET 3 AA6 7 THR B 30 CYS B 39 -1 N GLU B 38 O SER B 398 SHEET 4 AA6 7 VAL B 130 ASN B 136 -1 O VAL B 134 N SER B 35 SHEET 5 AA6 7 ILE B 114 ALA B 118 -1 N GLU B 115 O GLU B 135 SHEET 6 AA6 7 HIS B 459 LYS B 463 -1 O HIS B 459 N ALA B 118 SHEET 7 AA6 7 LYS B 466 VAL B 467 -1 O LYS B 466 N LYS B 463 SHEET 1 AA7 2 GLU B 56 VAL B 58 0 SHEET 2 AA7 2 VAL B 124 PRO B 126 -1 O ILE B 125 N THR B 57 SHEET 1 AA8 5 LEU B 190 ASP B 192 0 SHEET 2 AA8 5 ILE B 378 SER B 382 1 O PHE B 380 N HIS B 191 SHEET 3 AA8 5 LEU B 348 GLN B 352 1 N GLN B 352 O GLY B 381 SHEET 4 AA8 5 LEU B 308 ARG B 311 1 N ILE B 310 O ARG B 349 SHEET 5 AA8 5 VAL B 274 VAL B 277 1 N VAL B 274 O ILE B 309 SHEET 1 AA9 2 THR B 335 GLU B 336 0 SHEET 2 AA9 2 LYS B 342 LEU B 343 -1 O LEU B 343 N THR B 335 SHEET 1 AB1 2 SER B 431 ARG B 434 0 SHEET 2 AB1 2 PHE B 440 LEU B 443 -1 O VAL B 441 N HIS B 433 SITE 1 AC1 13 HIS A 191 PHE A 193 ARG A 196 ASP A 219 SITE 2 AC1 13 ALA A 244 SER A 275 ARG A 311 ILE A 351 SITE 3 AC1 13 ALA A 379 HOH A 617 HOH A 855 HOH A 876 SITE 4 AC1 13 TYR B 18 SITE 1 AC2 10 ARG A 392 SER A 398 LYS A 400 EDO A 504 SITE 2 AC2 10 HOH A 623 HOH A 772 HOH A 791 HOH A 856 SITE 3 AC2 10 ARG B 196 HOH B 644 SITE 1 AC3 11 ARG A 196 GLU A 246 HIS A 247 ARG A 311 SITE 2 AC3 11 ASP A 313 HOH A 640 HOH A 956 TYR B 18 SITE 3 AC3 11 HOH B 620 HOH B 698 HOH B 812 SITE 1 AC4 8 ARG A 40 ARG A 392 ASP A 393 ASN A 396 SITE 2 AC4 8 CYS A 397 SER A 398 PO4 A 502 HOH A 805 SITE 1 AC5 8 GLY A 315 PRO A 317 ASP A 354 GLY A 355 SITE 2 AC5 8 HOH A 646 HOH A 734 HOH A 871 HOH A 908 SITE 1 AC6 5 GLU A 187 VAL A 213 ASN A 214 LYS A 216 SITE 2 AC6 5 ARG A 477 SITE 1 AC7 6 PHE A 123 VAL A 124 ARG A 434 ASN A 479 SITE 2 AC7 6 HOH A 614 HOH A 784 SITE 1 AC8 7 GLY A 353 GLY A 355 GLY A 383 GLY A 384 SITE 2 AC8 7 HOH A 601 HOH A 625 HOH A 647 SITE 1 AC9 14 TYR A 18 HIS B 191 PHE B 193 ARG B 196 SITE 2 AC9 14 ASP B 219 VAL B 242 ALA B 244 SER B 275 SITE 3 AC9 14 ILE B 309 ARG B 311 ALA B 379 EDO B 504 SITE 4 AC9 14 HOH B 878 HOH B 973 SITE 1 AD1 10 TYR A 18 HOH A 623 HOH A 755 ARG B 196 SITE 2 AD1 10 GLU B 246 HIS B 247 ARG B 311 ASP B 313 SITE 3 AD1 10 HOH B 625 HOH B 644 SITE 1 AD2 10 ARG A 196 ARG B 392 SER B 398 LYS B 400 SITE 2 AD2 10 EDO B 505 HOH B 620 HOH B 675 HOH B 698 SITE 3 AD2 10 HOH B 747 HOH B 846 SITE 1 AD3 8 ARG A 392 PHE B 193 ARG B 196 6TA B 501 SITE 2 AD3 8 PO4 B 508 HOH B 644 HOH B 873 HOH B 928 SITE 1 AD4 8 ARG B 40 ARG B 392 ASP B 393 ASN B 396 SITE 2 AD4 8 CYS B 397 SER B 398 PO4 B 503 HOH B 920 SITE 1 AD5 7 HIS A 247 SER A 248 THR A 251 HOH A 956 SITE 2 AD5 7 LYS B 400 CYS B 401 PHE B 414 SITE 1 AD6 4 LYS A 77 GLU B 326 HOH B 631 HOH B 981 SITE 1 AD7 9 GLY B 353 GLY B 355 SER B 382 GLY B 383 SITE 2 AD7 9 GLY B 384 EDO B 504 HOH B 621 HOH B 659 SITE 3 AD7 9 HOH B 661 SITE 1 AD8 7 HOH A 645 GLY B 315 PRO B 317 ASP B 354 SITE 2 AD8 7 GLY B 355 HOH B 803 HOH B 941 CRYST1 60.748 106.589 83.320 90.00 96.65 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016461 0.000000 0.001920 0.00000 SCALE2 0.000000 0.009382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012083 0.00000