HEADER CELL CYCLE 09-SEP-21 7S4T TITLE CRYSTAL STRUCTURE OF CDK2 LIGANDED WITH COMPOUND EF2252 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, CDKN2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALLOSTERIC INHIBITOR, DRUG DEVELOPMENT, KINASE, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR L.SUN,E.SCHONBRUNN REVDAT 3 25-OCT-23 7S4T 1 REMARK REVDAT 2 15-MAR-23 7S4T 1 JRNL REVDAT 1 21-SEP-22 7S4T 0 JRNL AUTH E.B.FABER,N.WANG,K.JOHN,L.SUN,H.L.WONG,D.BURBAN,R.FRANCIS, JRNL AUTH 2 D.TIAN,K.H.HONG,A.YANG,L.WANG,M.ELSAID,H.KHALID, JRNL AUTH 3 N.M.LEVINSON,E.SCHONBRUNN,J.E.HAWKINSON,G.I.GEORG JRNL TITL SCREENING THROUGH LEAD OPTIMIZATION OF HIGH AFFINITY, JRNL TITL 2 ALLOSTERIC CYCLIN-DEPENDENT KINASE 2 (CDK2) INHIBITORS AS JRNL TITL 3 MALE CONTRACEPTIVES THAT REDUCE SPERM COUNTS IN MICE. JRNL REF J.MED.CHEM. V. 66 1928 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 36701569 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01731 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874_3874 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1052 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 41.5500 - 3.8200 1.00 2667 139 0.1601 0.1668 REMARK 3 2 3.8200 - 3.0300 1.00 2549 135 0.1763 0.2313 REMARK 3 3 3.0300 - 2.6500 1.00 2515 135 0.1965 0.2472 REMARK 3 4 2.6500 - 2.4100 1.00 2515 125 0.1872 0.2477 REMARK 3 5 2.4100 - 2.2300 1.00 2487 129 0.1732 0.2629 REMARK 3 6 2.2300 - 2.1000 1.00 2487 134 0.1689 0.2297 REMARK 3 7 2.1000 - 2.0000 1.00 2473 122 0.1658 0.1920 REMARK 3 8 2.0000 - 1.9100 1.00 2476 133 0.1772 0.2406 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7S4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000257920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21269 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4KD1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5MG/ML CDK2,1MM EF2252 SOAKING REMARK 280 48HOURS AT 0.1M HEPES NA, PH7.5, 10%(V/V)PEG3350, VAPOR REMARK 280 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 25.52350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.21550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.75750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.21550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.52350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.75750 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 TYR A 15 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 LYS A 9 CG CD CE NZ REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 150 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 157 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 162 CG CD OE1 OE2 REMARK 470 LYS A 278 CG CD CE NZ 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 8 137.91 -177.28 REMARK 500 THR A 72 -168.63 -126.67 REMARK 500 ARG A 126 -20.24 80.26 REMARK 500 ASP A 127 46.93 -144.12 REMARK 500 PRO A 254 42.54 -108.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 7S4T 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 EDO A 301 4 HET 88O A 302 25 HETNAM EDO 1,2-ETHANEDIOL HETNAM 88O 2-{[2-(6-CHLORO-1H-INDOL-3-YL)ETHYL]AMINO}-5- HETNAM 2 88O NITROBENZOIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 88O C17 H14 CL N3 O4 FORMUL 4 HOH *144(H2 O) HELIX 1 AA1 PRO A 45 LEU A 55 1 11 HELIX 2 AA2 LYS A 56 LEU A 58 5 3 HELIX 3 AA3 LEU A 87 ALA A 95 1 9 HELIX 4 AA4 PRO A 100 HIS A 121 1 22 HELIX 5 AA5 LYS A 129 GLN A 131 5 3 HELIX 6 AA6 LEU A 148 GLY A 153 1 6 HELIX 7 AA7 ALA A 170 LEU A 175 1 6 HELIX 8 AA8 THR A 182 ARG A 199 1 18 HELIX 9 AA9 SER A 207 GLY A 220 1 14 HELIX 10 AB1 GLY A 229 MET A 233 5 5 HELIX 11 AB2 ASP A 247 VAL A 252 1 6 HELIX 12 AB3 ASP A 256 LEU A 267 1 12 HELIX 13 AB4 SER A 276 LEU A 281 1 6 HELIX 14 AB5 ALA A 282 GLN A 287 5 6 SHEET 1 AA1 5 PHE A 4 GLY A 11 0 SHEET 2 AA1 5 VAL A 17 ASN A 23 -1 O LYS A 20 N VAL A 7 SHEET 3 AA1 5 VAL A 29 ARG A 36 -1 O LYS A 34 N VAL A 17 SHEET 4 AA1 5 LYS A 75 GLU A 81 -1 O PHE A 80 N ALA A 31 SHEET 5 AA1 5 LEU A 66 HIS A 71 -1 N ILE A 70 O TYR A 77 SHEET 1 AA2 3 GLN A 85 ASP A 86 0 SHEET 2 AA2 3 LEU A 133 ILE A 135 -1 O ILE A 135 N GLN A 85 SHEET 3 AA2 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 3.88 CRYST1 51.047 71.515 72.431 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 0.019590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013806 0.00000