PDB Short entry for 2XNM HEADER TRANSFERASE 05-AUG-10 2XNM TITLE STRUCTURE OF NEK2 BOUND TO CCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE NEK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, 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: 562 KEYWDS TRANSFERASE, CENTROSOME, MITOSIS, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR C.MAS-DROUX,R.BAYLISS REVDAT 1 30-MAR-11 2XNM 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. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.734 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.02 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.61 REMARK 3 NUMBER OF REFLECTIONS : 27237 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1649 REMARK 3 R VALUE (WORKING SET) : 0.1632 REMARK 3 FREE R VALUE : 0.1962 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1391 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 36.7412 - 3.9842 0.94 2635 139 0.1735 0.1984 REMARK 3 2 3.9842 - 3.1629 0.96 2614 152 0.1409 0.1721 REMARK 3 3 3.1629 - 2.7633 0.97 2639 137 0.1569 0.1682 REMARK 3 4 2.7633 - 2.5107 0.97 2690 122 0.1661 0.2242 REMARK 3 5 2.5107 - 2.3308 0.97 2617 149 0.1585 0.1883 REMARK 3 6 2.3308 - 2.1934 0.96 2601 159 0.1458 0.2090 REMARK 3 7 2.1934 - 2.0835 0.95 2580 133 0.1518 0.1687 REMARK 3 8 2.0835 - 1.9928 0.94 2545 119 0.1634 0.2027 REMARK 3 9 1.9928 - 1.9161 0.92 2497 144 0.1838 0.2474 REMARK 3 10 1.9161 - 1.8500 0.89 2428 137 0.1987 0.2122 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 : 0.351 REMARK 3 B_SOL : 60.098 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.21 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.9443 REMARK 3 B22 (A**2) : -3.8882 REMARK 3 B33 (A**2) : 4.8326 REMARK 3 B12 (A**2) : -0.0000 REMARK 3 B13 (A**2) : -4.5536 REMARK 3 B23 (A**2) : 0.0000 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 2237 REMARK 3 ANGLE : 1.022 3015 REMARK 3 CHIRALITY : 0.072 329 REMARK 3 PLANARITY : 0.004 376 REMARK 3 DIHEDRAL : 19.475 863 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): 29.4214 1.7458 -10.0301 REMARK 3 T TENSOR REMARK 3 T11: 0.1285 T22: 0.2602 REMARK 3 T33: 0.1931 T12: 0.0143 REMARK 3 T13: -0.0286 T23: 0.0592 REMARK 3 L TENSOR REMARK 3 L11: 2.2206 L22: 1.7983 REMARK 3 L33: 1.6366 L12: 0.4826 REMARK 3 L13: 1.4468 L23: -0.6335 REMARK 3 S TENSOR REMARK 3 S11: 0.0387 S12: -0.4716 S13: -0.3490 REMARK 3 S21: 0.1912 S22: 0.0046 S23: -0.2664 REMARK 3 S31: -0.0568 S32: -0.1947 S33: -0.0450 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 64:157) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1157 8.6281 -20.2626 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.0839 REMARK 3 T33: 0.0609 T12: 0.0034 REMARK 3 T13: 0.0019 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.6539 L22: 1.0494 REMARK 3 L33: 0.1905 L12: -0.8818 REMARK 3 L13: 0.1865 L23: 0.2739 REMARK 3 S TENSOR REMARK 3 S11: -0.0264 S12: -0.1606 S13: 0.0362 REMARK 3 S21: 0.0152 S22: 0.0469 S23: -0.1061 REMARK 3 S31: 0.0012 S32: 0.0411 S33: -0.0141 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 158:279) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5780 21.1165 -18.8555 REMARK 3 T TENSOR REMARK 3 T11: 0.0788 T22: 0.0883 REMARK 3 T33: 0.0381 T12: 0.0143 REMARK 3 T13: 0.0067 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.7269 L22: 2.0273 REMARK 3 L33: 0.4598 L12: -0.2553 REMARK 3 L13: -0.0238 L23: 0.0255 REMARK 3 S TENSOR REMARK 3 S11: -0.0626 S12: -0.1647 S13: -0.0077 REMARK 3 S21: 0.1743 S22: 0.0556 S23: 0.0028 REMARK 3 S31: -0.0388 S32: 0.0718 S33: 0.0015 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 1280) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0915 10.5869 -18.1903 REMARK 3 T TENSOR REMARK 3 T11: 0.2036 T22: 0.2939 REMARK 3 T33: 0.2992 T12: 0.0175 REMARK 3 T13: 0.0033 T23: -0.0706 REMARK 3 L TENSOR REMARK 3 L11: 5.4163 L22: 2.0460 REMARK 3 L33: 0.3230 L12: -1.0061 REMARK 3 L13: 0.1690 L23: 0.1134 REMARK 3 S TENSOR REMARK 3 S11: 0.0344 S12: -0.7903 S13: 0.9414 REMARK 3 S21: 0.0402 S22: -0.1886 S23: -0.0841 REMARK 3 S31: 0.2073 S32: 0.1996 S33: 0.0809 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 2XNM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-10. REMARK 100 THE PDBE ID CODE IS EBI-44920. 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27237 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.79 REMARK 200 RESOLUTION RANGE LOW (A) : 46.17 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.6 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.10 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.6 REMARK 200 R MERGE FOR SHELL (I) : 0.40 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.50 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.66 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 50.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.41500 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 SER A 131 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 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 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 CD NE CZ NH1 NH2 REMARK 470 SER A 18 OG REMARK 470 TYR A 19 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 60 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 79 CG OD1 ND2 REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 141 CG OD1 OD2 REMARK 470 ARG A 164 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 193 CG CD1 CD2 CE1 CE2 CZ OH 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 ASN A 189 25.87 -142.97 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 WGZ A1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1290 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1292 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A1291 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W5B RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ATPGAMMAS-BOUND REMARK 900 RELATED ID: 2XKC RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 14 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: 2W5H RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE APO REMARK 900 RELATED ID: 2XKD RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12 REMARK 900 RELATED ID: 2XK7 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 23 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: 2XNO RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT243779 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 DBREF 2XNM A 1 271 UNP P51955 NEK2_HUMAN 1 271 SEQADV 2XNM LEU A 272 UNP P51955 EXPRESSION TAG SEQADV 2XNM GLU A 273 UNP P51955 EXPRESSION TAG SEQADV 2XNM HIS A 274 UNP P51955 EXPRESSION TAG SEQADV 2XNM HIS A 275 UNP P51955 EXPRESSION TAG SEQADV 2XNM HIS A 276 UNP P51955 EXPRESSION TAG SEQADV 2XNM HIS A 277 UNP P51955 EXPRESSION TAG SEQADV 2XNM HIS A 278 UNP P51955 EXPRESSION TAG SEQADV 2XNM 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 WGZ A1280 38 HET EDO A1281 4 HET EDO A1282 4 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 CL A1289 1 HET CL A1290 1 HET TRS A1291 8 HET CL A1292 1 HETNAM WGZ 5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H- HETNAM 2 WGZ BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL) HETNAM 3 WGZ PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 2 WGZ C27 H27 F3 N4 O3 S FORMUL 3 EDO 8(C2 H6 O2) FORMUL 4 CL 3(CL 1-) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *260(H2 O) HELIX 1 1 ARG A 4 GLU A 6 5 3 HELIX 2 2 THR A 45 LEU A 62 1 18 HELIX 3 3 LEU A 94 ARG A 105 1 12 HELIX 4 4 ASP A 109 ARG A 130 1 22 HELIX 5 5 LYS A 143 ALA A 145 5 3 HELIX 6 6 ASP A 159 LEU A 166 1 8 HELIX 7 7 GLU A 186 ARG A 190 5 5 HELIX 8 8 ASN A 194 LEU A 212 1 19 HELIX 9 9 SER A 220 GLY A 231 1 12 HELIX 10 10 SER A 241 LEU A 252 1 12 HELIX 11 11 LYS A 255 ARG A 259 5 5 HELIX 12 12 SER A 261 GLU A 267 1 7 HELIX 13 13 LEU A 272 HIS A 276 5 5 SHEET 1 AA 5 TYR A 8 THR A 16 0 SHEET 2 AA 5 GLY A 20 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 LEU A 162 LEU A 166 HOH A2245 SITE 1 AC2 6 LEU A 11 LYS A 152 GLN A 153 HOH A2241 SITE 2 AC2 6 HOH A2246 HOH A2247 SITE 1 AC3 3 ILE A 247 GLU A 264 ASN A 268 SITE 1 AC4 6 ASP A 242 GLU A 243 GLU A 246 HIS A 277 SITE 2 AC4 6 HIS A 279 HOH A2249 SITE 1 AC5 6 TYR A 238 ARG A 239 SER A 241 HOH A2250 SITE 2 AC5 6 HOH A2251 HOH A2252 SITE 1 AC6 3 TYR A 12 ARG A 115 GLN A 153 SITE 1 AC7 7 ARG A 234 ARG A 235 TYR A 238 LEU A 266 SITE 2 AC7 7 HOH A2230 HOH A2254 HOH A2255 SITE 1 AC8 6 TYR A 181 TYR A 182 GLU A 208 PRO A 214 SITE 2 AC8 6 HOH A2257 HOH A2258 SITE 1 AC9 6 GLU A 195 LYS A 196 SER A 261 VAL A 262 SITE 2 AC9 6 HOH A2223 HOH A2259 SITE 1 BC1 2 GLU A 110 ARG A 239 SITE 1 BC2 3 ASN A 154 HIS A 277 HOH A2150 SITE 1 BC3 7 HIS A 128 ARG A 130 TYR A 193 ASN A 194 SITE 2 BC3 7 GLU A 195 ASP A 198 HOH A2260 CRYST1 100.800 56.830 81.300 90.00 133.21 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 0.009921 0.000000 0.009319 0.00000 SCALE2 0.000000 0.017596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016876 0.00000