HEADER TRANSFERASE/TRANSFERASE INHIBITOR 15-NOV-11 3UNK TITLE CDK2 IN COMPLEX WITH INHIBITOR YL5-083 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL DIVISION PROTEIN KINASE 2, P33 PROTEIN KINASE; COMPND 5 EC: 2.7.11.22; COMPND 6 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: CDK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TUNER(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS PROTEIN KINASE, ALLOSTERIC LIGAND, ANS, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.-Y.ZHU,M.P.MARTIN,R.ALAM,E.SCHONBRUNN REVDAT 3 13-SEP-23 3UNK 1 REMARK REVDAT 2 02-MAY-12 3UNK 1 JRNL REVDAT 1 25-JAN-12 3UNK 0 JRNL AUTH M.P.MARTIN,J.Y.ZHU,H.R.LAWRENCE,R.PIREDDU,Y.LUO,R.ALAM, JRNL AUTH 2 S.OZCAN,S.M.SEBTI,N.J.LAWRENCE,E.SCHONBRUNN JRNL TITL A NOVEL MECHANISM BY WHICH SMALL MOLECULE INHIBITORS INDUCE JRNL TITL 2 THE DFG FLIP IN AURORA A. JRNL REF ACS CHEM.BIOL. V. 7 698 2012 JRNL REFN ISSN 1554-8929 JRNL PMID 22248356 JRNL DOI 10.1021/CB200508B REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 835 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 18.7448 - 3.8071 1.00 2775 147 0.1732 0.2070 REMARK 3 2 3.8071 - 3.0259 1.00 2654 139 0.1802 0.2334 REMARK 3 3 3.0259 - 2.6446 1.00 2627 138 0.1856 0.2533 REMARK 3 4 2.6446 - 2.4034 1.00 2608 138 0.1783 0.2642 REMARK 3 5 2.4034 - 2.2314 1.00 2604 137 0.1779 0.2497 REMARK 3 6 2.2314 - 2.1000 1.00 2579 136 0.1766 0.2582 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 38.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 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) : -2.82210 REMARK 3 B22 (A**2) : -4.67290 REMARK 3 B33 (A**2) : 7.49500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.010 2462 REMARK 3 ANGLE : 1.305 3341 REMARK 3 CHIRALITY : 0.098 372 REMARK 3 PLANARITY : 0.008 421 REMARK 3 DIHEDRAL : 17.522 917 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 3UNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.23800 REMARK 200 R SYM FOR SHELL (I) : 0.29700 REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3PXR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MG/ML CDK2 PROTEIN, 1.5 MM YL5-83, 5 REMARK 280 % (V/V) PEG 3350, 50 MM HEPES/NAOH (PH 7.5), 50 MM PHOSPHATE (NA/ REMARK 280 K, PH 7.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.47500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.47500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.01000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 LEU A 37 REMARK 465 ASP A 38 REMARK 465 THR A 39 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 GLU A 40 CG CD OE1 OE2 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 LYS A 6 67.88 37.37 REMARK 500 GLU A 73 -136.86 52.43 REMARK 500 ARG A 126 -7.05 72.22 REMARK 500 ASP A 145 37.13 72.02 REMARK 500 THR A 158 -71.15 -71.31 REMARK 500 TYR A 159 -62.75 -133.02 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 0BY A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UNJ RELATED DB: PDB REMARK 900 RELATED ID: 3UNZ RELATED DB: PDB REMARK 900 RELATED ID: 3UO4 RELATED DB: PDB REMARK 900 RELATED ID: 3UO5 RELATED DB: PDB REMARK 900 RELATED ID: 3UO6 RELATED DB: PDB REMARK 900 RELATED ID: 3UOD RELATED DB: PDB REMARK 900 RELATED ID: 3UOH RELATED DB: PDB REMARK 900 RELATED ID: 3UOJ RELATED DB: PDB REMARK 900 RELATED ID: 3UOK RELATED DB: PDB REMARK 900 RELATED ID: 3UOL RELATED DB: PDB REMARK 900 RELATED ID: 3UP2 RELATED DB: PDB REMARK 900 RELATED ID: 3UP7 RELATED DB: PDB DBREF 3UNK A 1 298 UNP P24941 CDK2_HUMAN 1 298 SEQRES 1 A 298 MET GLU ASN PHE GLN LYS VAL GLU LYS ILE GLY GLU GLY SEQRES 2 A 298 THR TYR GLY VAL VAL TYR LYS ALA ARG ASN LYS LEU THR SEQRES 3 A 298 GLY GLU VAL VAL ALA LEU LYS LYS ILE ARG LEU ASP THR SEQRES 4 A 298 GLU THR GLU GLY VAL PRO SER THR ALA ILE ARG GLU ILE SEQRES 5 A 298 SER LEU LEU LYS GLU LEU ASN HIS PRO ASN ILE VAL LYS SEQRES 6 A 298 LEU LEU ASP VAL ILE HIS THR GLU ASN LYS LEU TYR LEU SEQRES 7 A 298 VAL PHE GLU PHE LEU HIS GLN ASP LEU LYS LYS PHE MET SEQRES 8 A 298 ASP ALA SER ALA LEU THR GLY ILE PRO LEU PRO LEU ILE SEQRES 9 A 298 LYS SER TYR LEU PHE GLN LEU LEU GLN GLY LEU ALA PHE SEQRES 10 A 298 CYS HIS SER HIS ARG VAL LEU HIS ARG ASP LEU LYS PRO SEQRES 11 A 298 GLN ASN LEU LEU ILE ASN THR GLU GLY ALA ILE LYS LEU SEQRES 12 A 298 ALA ASP PHE GLY LEU ALA ARG ALA PHE GLY VAL PRO VAL SEQRES 13 A 298 ARG THR TYR THR HIS GLU VAL VAL THR LEU TRP TYR ARG SEQRES 14 A 298 ALA PRO GLU ILE LEU LEU GLY CYS LYS TYR TYR SER THR SEQRES 15 A 298 ALA VAL ASP ILE TRP SER LEU GLY CYS ILE PHE ALA GLU SEQRES 16 A 298 MET VAL THR ARG ARG ALA LEU PHE PRO GLY ASP SER GLU SEQRES 17 A 298 ILE ASP GLN LEU PHE ARG ILE PHE ARG THR LEU GLY THR SEQRES 18 A 298 PRO ASP GLU VAL VAL TRP PRO GLY VAL THR SER MET PRO SEQRES 19 A 298 ASP TYR LYS PRO SER PHE PRO LYS TRP ALA ARG GLN ASP SEQRES 20 A 298 PHE SER LYS VAL VAL PRO PRO LEU ASP GLU ASP GLY ARG SEQRES 21 A 298 SER LEU LEU SER GLN MET LEU HIS TYR ASP PRO ASN LYS SEQRES 22 A 298 ARG ILE SER ALA LYS ALA ALA LEU ALA HIS PRO PHE PHE SEQRES 23 A 298 GLN ASP VAL THR LYS PRO VAL PRO HIS LEU ARG LEU HET 0BY A 299 24 HET PO4 A 300 5 HETNAM 0BY 4-({4-[(2-CHLOROPHENYL)AMINO]PYRIMIDIN-2-YL}AMINO) HETNAM 2 0BY BENZOIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 2 0BY C17 H13 CL N4 O2 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *153(H2 O) HELIX 1 1 PRO A 45 LYS A 56 1 12 HELIX 2 2 LEU A 87 SER A 94 1 8 HELIX 3 3 PRO A 100 HIS A 121 1 22 HELIX 4 4 LYS A 129 GLN A 131 5 3 HELIX 5 5 GLY A 147 GLY A 153 1 7 HELIX 6 6 ALA A 170 LEU A 175 1 6 HELIX 7 7 THR A 182 ARG A 199 1 18 HELIX 8 8 SER A 207 GLY A 220 1 14 HELIX 9 9 GLY A 229 MET A 233 5 5 HELIX 10 10 ASP A 247 VAL A 251 5 5 HELIX 11 11 ASP A 256 LEU A 267 1 12 HELIX 12 12 SER A 276 LEU A 281 1 6 HELIX 13 13 ALA A 282 GLN A 287 5 6 SHEET 1 A 5 GLU A 8 GLY A 13 0 SHEET 2 A 5 GLY A 16 ARG A 22 -1 O VAL A 18 N GLY A 11 SHEET 3 A 5 VAL A 29 ILE A 35 -1 O LEU A 32 N TYR A 19 SHEET 4 A 5 LYS A 75 GLU A 81 -1 O LEU A 76 N ILE A 35 SHEET 5 A 5 LEU A 66 THR A 72 -1 N LEU A 67 O VAL A 79 SHEET 1 B 3 GLN A 85 ASP A 86 0 SHEET 2 B 3 LEU A 133 ILE A 135 -1 O ILE A 135 N GLN A 85 SHEET 3 B 3 ILE A 141 LEU A 143 -1 O LYS A 142 N LEU A 134 SITE 1 AC1 16 ILE A 10 VAL A 18 ALA A 31 LYS A 33 SITE 2 AC1 16 PHE A 80 GLU A 81 PHE A 82 LEU A 83 SITE 3 AC1 16 HIS A 84 LYS A 89 GLN A 131 ASN A 132 SITE 4 AC1 16 LEU A 134 ASP A 145 HOH A 365 HOH A 376 SITE 1 AC2 10 GLY A 13 THR A 14 TYR A 15 LYS A 33 SITE 2 AC2 10 ASP A 127 LYS A 129 ASN A 132 ASP A 145 SITE 3 AC2 10 HOH A 369 HOH A 394 CRYST1 52.950 72.020 72.370 90.00 90.00 90.00 P 21 21 21 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 0.018886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013818 0.00000