HEADER CELL CYCLE 19-AUG-21 7RWE TITLE CRYSTAL STRUCTURE OF CDK2 LIGANDED WITH COMPOUND GPHR787 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 7RWE 1 REMARK REVDAT 2 15-MAR-23 7RWE 1 JRNL REVDAT 1 24-AUG-22 7RWE 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. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 38699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1006 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 43.2500 - 3.0400 0.99 5603 149 0.2087 0.2215 REMARK 3 2 3.0400 - 2.4100 1.00 5438 145 0.2334 0.2530 REMARK 3 3 2.4100 - 2.1100 1.00 5379 144 0.2145 0.2651 REMARK 3 4 2.1100 - 1.9200 0.99 5328 142 0.2181 0.2302 REMARK 3 5 1.9200 - 1.7800 1.00 5335 143 0.2200 0.2500 REMARK 3 6 1.7800 - 1.6700 1.00 5310 141 0.2241 0.2858 REMARK 3 7 1.6700 - 1.5900 1.00 5300 142 0.2050 0.2278 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.25 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 7RWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000257771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 170 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) : 1.54178 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 72.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05400 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: PHENIX REMARK 200 STARTING MODEL: 4KD1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5MG/ML CDK2 PROTEIN CRYSTALIZED AT REMARK 280 0.1M HEPES NA, PH7.5, 10%PEG3350 CONDITION, THEN SOAKED WITH REMARK 280 10MM GPHR787 FOR 24 HOURS, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 26.94000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.26000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.26000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.94000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.19000 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 GLU A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 TYR A 15 REMARK 465 LYS A 24 REMARK 465 LEU A 25 REMARK 465 THR A 26 REMARK 465 ARG A 36 REMARK 465 LEU A 37 REMARK 465 ASP A 38 REMARK 465 THR A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 GLU A 42 REMARK 465 GLY A 43 REMARK 465 VAL A 44 REMARK 465 PRO A 45 REMARK 465 SER A 46 REMARK 465 THR A 47 REMARK 465 ALA A 48 REMARK 465 ILE A 49 REMARK 465 ARG A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 73 REMARK 465 ASN A 74 REMARK 465 LYS A 75 REMARK 465 ALA A 149 REMARK 465 ARG A 150 REMARK 465 ALA A 151 REMARK 465 PHE A 152 REMARK 465 GLY A 153 REMARK 465 VAL A 154 REMARK 465 PRO A 155 REMARK 465 VAL A 156 REMARK 465 ARG A 157 REMARK 465 THR A 158 REMARK 465 TYR A 159 REMARK 465 THR A 160 REMARK 465 HIS A 161 REMARK 465 GLU A 162 REMARK 465 VAL A 163 REMARK 465 VAL A 164 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 GLN A 5 CG CD OE1 NE2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 247 CG OD1 OD2 REMARK 470 GLU A 257 CG CD OE1 OE2 REMARK 470 ARG A 297 CG 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 ARG A 126 -19.03 80.54 REMARK 500 ASP A 127 45.84 -140.30 REMARK 500 TYR A 179 60.52 -115.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RWE 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 7TH A 301 22 HET 7TH A 302 22 HETNAM 7TH 5-NITRO-2-[(3-PHENYLPROPYL)AMINO]BENZOIC ACID FORMUL 2 7TH 2(C16 H16 N2 O4) FORMUL 4 HOH *66(H2 O) HELIX 1 AA1 ILE A 52 LEU A 58 5 7 HELIX 2 AA2 LEU A 87 SER A 94 1 8 HELIX 3 AA3 PRO A 100 HIS A 121 1 22 HELIX 4 AA4 LYS A 129 GLN A 131 5 3 HELIX 5 AA5 ALA A 170 LEU A 175 1 6 HELIX 6 AA6 THR A 182 ARG A 199 1 18 HELIX 7 AA7 SER A 207 GLY A 220 1 14 HELIX 8 AA8 GLY A 229 MET A 233 5 5 HELIX 9 AA9 ASP A 247 VAL A 251 5 5 HELIX 10 AB1 ASP A 256 LEU A 267 1 12 HELIX 11 AB2 SER A 276 ALA A 282 1 7 HELIX 12 AB3 HIS A 283 GLN A 287 5 5 SHEET 1 AA1 5 GLN A 5 GLY A 11 0 SHEET 2 AA1 5 VAL A 17 ARG A 22 -1 O LYS A 20 N VAL A 7 SHEET 3 AA1 5 VAL A 29 LYS A 34 -1 O LEU A 32 N TYR A 19 SHEET 4 AA1 5 TYR A 77 GLU A 81 -1 O LEU A 78 N LYS A 33 SHEET 5 AA1 5 LEU A 66 ILE A 70 -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 CRYST1 53.880 72.380 72.520 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 0.018560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013816 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013789 0.00000