PDB Short entry for 2XNO HEADER TRANSFERASE 05-AUG-10 2XNO TITLE STRUCTURE OF NEK2 BOUND TO CCT243779 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE NEK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-271; COMPND 5 SYNONYM: NEVER IN MITOSIS A-RELATED KINASE 2, NEK2, NIMA-RELATED COMPND 6 PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, HSPK 21; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET30 KEYWDS TRANSFERASE, CENTROSOME, MITOSIS, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR C.MAS-DROUX,R.BAYLISS REVDAT 2 20-DEC-23 2XNO 1 REMARK REVDAT 1 30-MAR-11 2XNO 0 JRNL AUTH S.SOLANKI,P.INNOCENTI,C.MAS-DROUX,K.BOXALL,C.BARILLARI, JRNL AUTH 2 R.L.VAN MONTFORT,G.W.AHERNE,R.BAYLISS,S.HOELDER JRNL TITL BENZIMIDAZOLE INHIBITORS INDUCE A DFG-OUT CONFORMATION OF JRNL TITL 2 NEVER IN MITOSIS GENE A-RELATED KINASE 2 (NEK2) WITHOUT JRNL TITL 3 BINDING TO THE BACK POCKET AND REVEAL A NONLINEAR JRNL TITL 4 STRUCTURE-ACTIVITY RELATIONSHIP. JRNL REF J.MED.CHEM. V. 54 1626 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21366329 JRNL DOI 10.1021/JM1011726 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 22423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1136 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 36.6801 - 3.9586 0.97 2760 153 0.1775 0.2098 REMARK 3 2 3.9586 - 3.1426 0.98 2716 152 0.1580 0.2041 REMARK 3 3 3.1426 - 2.7455 0.98 2712 139 0.1733 0.2123 REMARK 3 4 2.7455 - 2.4946 0.96 2715 124 0.1782 0.2380 REMARK 3 5 2.4946 - 2.3158 0.96 2632 162 0.1622 0.2260 REMARK 3 6 2.3158 - 2.1793 0.95 2627 152 0.1604 0.1976 REMARK 3 7 2.1793 - 2.0701 0.93 2564 124 0.1607 0.1969 REMARK 3 8 2.0701 - 1.9800 0.92 2561 130 0.1681 0.2120 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 45.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.50860 REMARK 3 B22 (A**2) : -4.17760 REMARK 3 B33 (A**2) : 5.68630 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.99860 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 : 0.007 2156 REMARK 3 ANGLE : 1.092 2890 REMARK 3 CHIRALITY : 0.074 311 REMARK 3 PLANARITY : 0.006 362 REMARK 3 DIHEDRAL : 21.276 817 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 3:63) REMARK 3 ORIGIN FOR THE GROUP (A): -29.6196 1.3912 9.8182 REMARK 3 T TENSOR REMARK 3 T11: 0.1355 T22: 0.2948 REMARK 3 T33: 0.1644 T12: -0.0358 REMARK 3 T13: -0.0261 T23: -0.0673 REMARK 3 L TENSOR REMARK 3 L11: 1.4651 L22: 0.9594 REMARK 3 L33: 0.7248 L12: -0.4463 REMARK 3 L13: 0.6953 L23: 0.2015 REMARK 3 S TENSOR REMARK 3 S11: -0.0226 S12: 0.6150 S13: -0.4183 REMARK 3 S21: -0.2234 S22: 0.0474 S23: 0.3143 REMARK 3 S31: 0.0108 S32: 0.0865 S33: -0.0173 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 64:157) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1849 8.6155 20.2146 REMARK 3 T TENSOR REMARK 3 T11: 0.0433 T22: 0.1023 REMARK 3 T33: 0.0907 T12: -0.0087 REMARK 3 T13: 0.0189 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 0.7196 L22: 0.6292 REMARK 3 L33: 0.3480 L12: 0.6383 REMARK 3 L13: -0.2130 L23: -0.0727 REMARK 3 S TENSOR REMARK 3 S11: -0.0683 S12: 0.1434 S13: 0.1083 REMARK 3 S21: 0.0126 S22: 0.0322 S23: 0.1877 REMARK 3 S31: 0.0145 S32: -0.0696 S33: 0.0270 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 158:279) REMARK 3 ORIGIN FOR THE GROUP (A): -5.8552 21.3938 19.5172 REMARK 3 T TENSOR REMARK 3 T11: 0.0836 T22: 0.1027 REMARK 3 T33: 0.0515 T12: -0.0079 REMARK 3 T13: 0.0293 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.3839 L22: 0.7718 REMARK 3 L33: 0.2517 L12: 0.4196 REMARK 3 L13: -0.0612 L23: 0.1935 REMARK 3 S TENSOR REMARK 3 S11: -0.0693 S12: 0.1712 S13: -0.0022 REMARK 3 S21: -0.0733 S22: 0.0467 S23: -0.0378 REMARK 3 S31: -0.0502 S32: -0.0611 S33: -0.0006 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 1280) REMARK 3 ORIGIN FOR THE GROUP (A): -26.0841 10.0175 17.8905 REMARK 3 T TENSOR REMARK 3 T11: 0.0832 T22: 0.3101 REMARK 3 T33: 0.7055 T12: -0.0702 REMARK 3 T13: 0.0055 T23: 0.1557 REMARK 3 L TENSOR REMARK 3 L11: 0.0098 L22: 0.1512 REMARK 3 L33: 0.2808 L12: 0.0011 REMARK 3 L13: -0.0202 L23: 0.0679 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: 0.1448 S13: 0.0926 REMARK 3 S21: 0.0306 S22: 0.0690 S23: 0.1110 REMARK 3 S31: -0.0307 S32: 0.0012 S33: -0.1458 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 2XNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1290044972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30461 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2W5A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.52500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.52500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.44000 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 PRO A 2 REMARK 465 ASP A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 HIS A 135 REMARK 465 THR A 136 REMARK 465 VAL A 137 REMARK 465 LEU A 138 REMARK 465 HIS A 139 REMARK 465 GLY A 161 REMARK 465 LEU A 162 REMARK 465 ALA A 163 REMARK 465 ARG A 164 REMARK 465 ILE A 165 REMARK 465 LEU A 166 REMARK 465 ASN A 167 REMARK 465 HIS A 168 REMARK 465 ASP A 169 REMARK 465 THR A 170 REMARK 465 SER A 171 REMARK 465 PHE A 172 REMARK 465 ALA A 173 REMARK 465 LYS A 174 REMARK 465 THR A 175 REMARK 465 MET A 191 REMARK 465 SER A 192 REMARK 465 TYR A 193 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 19 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 60 CD NE CZ NH1 NH2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 LEU A 62 CG CD1 CD2 REMARK 470 LYS A 63 CD CE NZ REMARK 470 ARG A 73 CD NE CZ NH1 NH2 REMARK 470 ILE A 75 CG1 CG2 CD1 REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 79 CG OD1 ND2 REMARK 470 ARG A 130 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 160 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 190 CD NE CZ NH1 NH2 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 LEU A 142 49.88 -94.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ED8 A 1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1289 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1291 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1295 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XKC RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 14 REMARK 900 RELATED ID: 2W5B RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ATPGAMMAS-BOUND REMARK 900 RELATED ID: 2XNP RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT244858 REMARK 900 RELATED ID: 2WQO RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO THE AMINOPYRIDINE CCT241950 REMARK 900 RELATED ID: 2JAV RELATED DB: PDB REMARK 900 HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND REMARK 900 RELATED ID: 2XKE RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINIPYRAZINE COMPOUND 5 REMARK 900 RELATED ID: 2XK7 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 23 REMARK 900 RELATED ID: 2XKD RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12 REMARK 900 RELATED ID: 2W5H RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE APO REMARK 900 RELATED ID: 2XKF RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 2 REMARK 900 RELATED ID: 2XK8 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 15 REMARK 900 RELATED ID: 2XK6 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 36 REMARK 900 RELATED ID: 2XNN RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT242430 REMARK 900 RELATED ID: 2XK4 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 17 REMARK 900 RELATED ID: 2XK3 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 35 REMARK 900 RELATED ID: 2W5A RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ADP-BOUND REMARK 900 RELATED ID: 2XNM RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT DBREF 2XNO A 1 271 UNP P51955 NEK2_HUMAN 1 271 SEQADV 2XNO LEU A 272 UNP P51955 EXPRESSION TAG SEQADV 2XNO GLU A 273 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 274 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 275 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 276 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 277 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 278 UNP P51955 EXPRESSION TAG SEQADV 2XNO HIS A 279 UNP P51955 EXPRESSION TAG SEQRES 1 A 279 MET PRO SER ARG ALA GLU ASP TYR GLU VAL LEU TYR THR SEQRES 2 A 279 ILE GLY THR GLY SER TYR GLY ARG CYS GLN LYS ILE ARG SEQRES 3 A 279 ARG LYS SER ASP GLY LYS ILE LEU VAL TRP LYS GLU LEU SEQRES 4 A 279 ASP TYR GLY SER MET THR GLU ALA GLU LYS GLN MET LEU SEQRES 5 A 279 VAL SER GLU VAL ASN LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 6 A 279 ASN ILE VAL ARG TYR TYR ASP ARG ILE ILE ASP ARG THR SEQRES 7 A 279 ASN THR THR LEU TYR ILE VAL MET GLU TYR CYS GLU GLY SEQRES 8 A 279 GLY ASP LEU ALA SER VAL ILE THR LYS GLY THR LYS GLU SEQRES 9 A 279 ARG GLN TYR LEU ASP GLU GLU PHE VAL LEU ARG VAL MET SEQRES 10 A 279 THR GLN LEU THR LEU ALA LEU LYS GLU CYS HIS ARG ARG SEQRES 11 A 279 SER ASP GLY GLY HIS THR VAL LEU HIS ARG ASP LEU LYS SEQRES 12 A 279 PRO ALA ASN VAL PHE LEU ASP GLY LYS GLN ASN VAL LYS SEQRES 13 A 279 LEU GLY ASP PHE GLY LEU ALA ARG ILE LEU ASN HIS ASP SEQRES 14 A 279 THR SER PHE ALA LYS THR PHE VAL GLY THR PRO TYR TYR SEQRES 15 A 279 MET SER PRO GLU GLN MET ASN ARG MET SER TYR ASN GLU SEQRES 16 A 279 LYS SER ASP ILE TRP SER LEU GLY CYS LEU LEU TYR GLU SEQRES 17 A 279 LEU CYS ALA LEU MET PRO PRO PHE THR ALA PHE SER GLN SEQRES 18 A 279 LYS GLU LEU ALA GLY LYS ILE ARG GLU GLY LYS PHE ARG SEQRES 19 A 279 ARG ILE PRO TYR ARG TYR SER ASP GLU LEU ASN GLU ILE SEQRES 20 A 279 ILE THR ARG MET LEU ASN LEU LYS ASP TYR HIS ARG PRO SEQRES 21 A 279 SER VAL GLU GLU ILE LEU GLU ASN PRO LEU ILE LEU GLU SEQRES 22 A 279 HIS HIS HIS HIS HIS HIS HET ED8 A1280 37 HET CL A1281 1 HET CL A1282 1 HET EDO A1283 4 HET EDO A1284 4 HET EDO A1285 4 HET EDO A1286 4 HET EDO A1287 4 HET EDO A1288 4 HET EDO A1289 4 HET EDO A1290 4 HET EDO A1291 4 HET GOL A1292 6 HET DMS A1293 4 HET EDO A1294 4 HET EDO A1295 4 HETNAM ED8 5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1- HETNAM 2 ED8 YL}-3-{[2-(TRIFLUOROMETHYL)BENZYL]OXY}THIOPHENE-2- HETNAM 3 ED8 CARBOXAMIDE HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ED8 C26 H25 F3 N4 O3 S FORMUL 3 CL 2(CL 1-) FORMUL 5 EDO 11(C2 H6 O2) FORMUL 14 GOL C3 H8 O3 FORMUL 15 DMS C2 H6 O S FORMUL 18 HOH *207(H2 O) HELIX 1 1 ARG A 4 GLU A 6 5 3 HELIX 2 2 THR A 45 ARG A 60 1 16 HELIX 3 3 LEU A 94 ARG A 105 1 12 HELIX 4 4 ASP A 109 SER A 131 1 23 HELIX 5 5 LYS A 143 ALA A 145 5 3 HELIX 6 6 SER A 184 ASN A 189 1 6 HELIX 7 7 ASN A 194 LEU A 212 1 19 HELIX 8 8 SER A 220 GLY A 231 1 12 HELIX 9 9 SER A 241 LEU A 252 1 12 HELIX 10 10 LYS A 255 ARG A 259 5 5 HELIX 11 11 SER A 261 GLU A 267 1 7 HELIX 12 12 LEU A 272 HIS A 276 5 5 SHEET 1 AA 5 TYR A 8 GLY A 15 0 SHEET 2 AA 5 ARG A 21 ARG A 27 -1 O CYS A 22 N ILE A 14 SHEET 3 AA 5 ILE A 33 ASP A 40 -1 O LEU A 34 N ILE A 25 SHEET 4 AA 5 THR A 81 GLU A 87 -1 O LEU A 82 N LEU A 39 SHEET 5 AA 5 TYR A 70 ASP A 76 -1 N TYR A 71 O VAL A 85 SHEET 1 AB 3 GLY A 92 ASP A 93 0 SHEET 2 AB 3 VAL A 147 LEU A 149 -1 N LEU A 149 O GLY A 92 SHEET 3 AB 3 VAL A 155 LEU A 157 -1 O LYS A 156 N PHE A 148 SITE 1 AC1 16 ILE A 14 GLY A 15 CYS A 22 LYS A 37 SITE 2 AC1 16 GLU A 87 TYR A 88 CYS A 89 ASP A 93 SITE 3 AC1 16 SER A 96 ALA A 145 PHE A 148 GLY A 158 SITE 4 AC1 16 ASP A 159 EDO A1294 HOH A2034 HOH A2194 SITE 1 AC2 3 GLU A 110 ARG A 239 HOH A2064 SITE 1 AC3 6 LEU A 11 LYS A 152 GLN A 153 HOH A2190 SITE 2 AC3 6 HOH A2195 HOH A2196 SITE 1 AC4 4 TYR A 181 GLU A 208 PRO A 214 HOH A2197 SITE 1 AC5 5 GLU A 195 LYS A 196 SER A 261 VAL A 262 SITE 2 AC5 5 HOH A2198 SITE 1 AC6 7 ARG A 234 ARG A 235 TYR A 238 LEU A 266 SITE 2 AC6 7 EDO A1289 EDO A1290 HOH A2199 SITE 1 AC7 5 TYR A 238 ASP A 242 HOH A2104 HOH A2202 SITE 2 AC7 5 HOH A2203 SITE 1 AC8 3 ILE A 247 GLU A 264 ASN A 268 SITE 1 AC9 9 ARG A 234 ARG A 235 TYR A 238 LEU A 266 SITE 2 AC9 9 ILE A 271 LEU A 272 GLU A 273 HIS A 276 SITE 3 AC9 9 EDO A1286 SITE 1 BC1 6 TYR A 207 ALA A 211 ARG A 235 ILE A 236 SITE 2 BC1 6 EDO A1286 HOH A2129 SITE 1 BC2 6 ASP A 242 GLU A 246 HIS A 277 HIS A 279 SITE 2 BC2 6 HOH A2154 HOH A2205 SITE 1 BC3 6 ARG A 140 ASP A 159 PHE A 160 HOH A2114 SITE 2 BC3 6 HOH A2206 HOH A2207 SITE 1 BC4 5 PRO A 65 ASN A 154 LYS A 156 HIS A 277 SITE 2 BC4 5 HIS A 279 SITE 1 BC5 2 ASP A 159 ED8 A1280 SITE 1 BC6 1 PHE A 160 CRYST1 101.050 56.880 81.340 90.00 133.46 90.00 C 1 2 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 0.009896 0.000000 0.009378 0.00000 SCALE2 0.000000 0.017581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016937 0.00000