HEADER TRANSFERASE 18-JAN-05 1YKR TITLE CRYSTAL STRUCTURE OF CDK2 WITH AN AMINOIMIDAZO PYRIDINE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION PROTEIN KINASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P33 PROTEIN KINASE; COMPND 5 EC: 2.7.1.37; 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: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS KEYWDS CELL CYCLE DIVISION PROTEIN KINASE 2, CDK2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.HAMDOUCHI,B.ZHONG,J.MENDOZA,C.JARAMILLO,F.ZHANG,H.B.BROOKS REVDAT 3 23-AUG-23 1YKR 1 REMARK REVDAT 2 24-FEB-09 1YKR 1 VERSN REVDAT 1 24-JAN-06 1YKR 0 JRNL AUTH C.HAMDOUCHI,B.ZHONG,J.MENDOZA,E.COLLINS,C.JARAMILLO, JRNL AUTH 2 J.E.DE DIEGO,D.ROBERTSON,C.D.SPENCER,B.D.ANDERSON, JRNL AUTH 3 S.A.WATKINS,F.ZHANG,H.B.BROOKS JRNL TITL STRUCTURE-BASED DESIGN OF A NEW CLASS OF HIGHLY SELECTIVE JRNL TITL 2 AMINOIMIDAZO[1,2-A]PYRIDINE-BASED INHIBITORS OF CYCLIN JRNL TITL 3 DEPENDENT KINASES JRNL REF BIOORG.MED.CHEM.LETT. V. 15 1943 2005 JRNL REFN ISSN 0960-894X JRNL PMID 15780638 JRNL DOI 10.1016/J.BMCL.2005.01.052 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25791 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHTOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1244 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2398 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.16300 REMARK 3 B22 (A**2) : -8.40600 REMARK 3 B33 (A**2) : 6.24300 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.04 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.05 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.098 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.952 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE REMARK 4 REMARK 4 1YKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25791 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1HCK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3000, 100MM HEPES, 200MM NACL, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K 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 26.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.70900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.69650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.70900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.69650 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 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 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 GLU A 8 144.38 -175.93 REMARK 500 LYS A 20 55.90 -109.41 REMARK 500 ASP A 38 -157.35 -71.93 REMARK 500 GLU A 42 -91.49 -159.07 REMARK 500 VAL A 44 121.30 -34.06 REMARK 500 THR A 72 166.74 -45.30 REMARK 500 GLU A 73 18.38 52.09 REMARK 500 ARG A 126 -24.18 83.53 REMARK 500 PHE A 152 -90.19 -107.84 REMARK 500 ARG A 199 32.00 70.58 REMARK 500 PRO A 254 42.23 -102.99 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 628 A 299 DBREF 1YKR 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 628 A 299 30 HETNAM 628 4-{[6-(2,6-DICHLOROBENZOYL)IMIDAZO[1,2-A]PYRIDIN-2- HETNAM 2 628 YL]AMINO}BENZENESULFONAMIDE HETSYN 628 PHENYLAMINOIMIDAZO(1,2-ALPHA)PYRIDINE FORMUL 2 628 C20 H14 CL2 N4 O3 S FORMUL 3 HOH *102(H2 O) HELIX 1 1 PRO A 45 LYS A 56 1 12 HELIX 2 2 HIS A 71 LYS A 75 5 5 HELIX 3 3 LEU A 87 SER A 94 1 8 HELIX 4 4 PRO A 100 HIS A 121 1 22 HELIX 5 5 LYS A 129 GLN A 131 5 3 HELIX 6 6 GLY A 147 PHE A 152 1 6 HELIX 7 7 ALA A 170 LEU A 175 1 6 HELIX 8 8 THR A 182 ARG A 199 1 18 HELIX 9 9 SER A 207 GLY A 220 1 14 HELIX 10 10 GLY A 229 MET A 233 5 5 HELIX 11 11 ASP A 247 VAL A 252 1 6 HELIX 12 12 ASP A 256 LEU A 267 1 12 HELIX 13 13 SER A 276 ALA A 282 1 7 HELIX 14 14 HIS A 283 GLN A 287 5 5 SHEET 1 A 2 PHE A 4 GLN A 5 0 SHEET 2 A 2 ARG A 22 ASN A 23 -1 O ARG A 22 N GLN A 5 SHEET 1 B 5 LYS A 9 GLY A 11 0 SHEET 2 B 5 GLY A 16 TYR A 19 -1 O VAL A 18 N GLY A 11 SHEET 3 B 5 VAL A 30 ILE A 35 -1 O LEU A 32 N TYR A 19 SHEET 4 B 5 LEU A 76 GLU A 81 -1 O LEU A 76 N ILE A 35 SHEET 5 B 5 LEU A 66 ILE A 70 -1 N ASP A 68 O VAL A 79 SHEET 1 C 3 GLN A 85 ASP A 86 0 SHEET 2 C 3 LEU A 133 ILE A 135 -1 O ILE A 135 N GLN A 85 SHEET 3 C 3 ILE A 141 LEU A 143 -1 O LYS A 142 N LEU A 134 CISPEP 1 PRO A 253 PRO A 254 0 0.35 SITE 1 AC1 15 VAL A 18 ALA A 31 LYS A 33 VAL A 64 SITE 2 AC1 15 PHE A 80 GLU A 81 PHE A 82 LEU A 83 SITE 3 AC1 15 HIS A 84 GLN A 85 ASP A 86 LYS A 89 SITE 4 AC1 15 LEU A 134 ALA A 144 ASP A 145 CRYST1 53.250 71.393 71.418 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 0.018779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014002 0.00000