HEADER CELL CYCLE 21-SEP-21 7SA0 TITLE CRYSTAL STRUCTURE OF CDK2 LIGANDED WITH COMPOUND EF4195 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 2 18-OCT-23 7SA0 1 REMARK REVDAT 1 05-OCT-22 7SA0 0 JRNL AUTH L.SUN,E.SCHONBRUNN JRNL TITL DEVELOPMENT OF SELECTIVE ALLOSTERIC INHIBITORS OF JRNL TITL 2 CYCLIN-DEPENDENT KINASE 2 (CDK2) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.59 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.330 REMARK 3 FREE R VALUE TEST SET COUNT : 2436 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 37.1500 - 4.0900 1.00 4157 147 0.1676 0.1735 REMARK 3 2 4.0900 - 3.2400 1.00 4200 145 0.1840 0.1887 REMARK 3 3 3.2400 - 2.8300 1.00 4167 138 0.2038 0.2234 REMARK 3 4 2.8300 - 2.5800 1.00 4166 149 0.1966 0.2591 REMARK 3 5 2.5800 - 2.3900 1.00 4209 151 0.2018 0.2497 REMARK 3 6 2.3900 - 2.2500 1.00 4172 146 0.1967 0.1914 REMARK 3 7 2.2500 - 2.1400 1.00 4185 142 0.2023 0.2351 REMARK 3 8 2.1400 - 2.0400 1.00 4186 146 0.2036 0.2737 REMARK 3 9 2.0400 - 1.9700 0.99 4152 132 0.2042 0.2657 REMARK 3 10 1.9700 - 1.9000 1.00 4198 138 0.2061 0.2833 REMARK 3 11 1.9000 - 1.8400 1.00 4178 135 0.2173 0.2227 REMARK 3 12 1.8400 - 1.7900 1.00 4197 147 0.2165 0.2514 REMARK 3 13 1.7900 - 1.7400 1.00 4142 148 0.2222 0.2792 REMARK 3 14 1.7400 - 1.7000 1.00 4207 141 0.2285 0.2675 REMARK 3 15 1.7000 - 1.6600 1.00 4195 154 0.2355 0.2886 REMARK 3 16 1.6600 - 1.6200 0.98 4105 131 0.2394 0.2653 REMARK 3 17 1.6200 - 1.5900 0.94 3922 146 0.2680 0.3284 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) : 26.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.09 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 7SA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000258330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-21 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51270 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 54.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 54.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 49.50 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 (%): 40.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5MG/ML CDK2 CRYSTALIZED IN 50MM REMARK 280 NA/KPO4, PH6.9, 50MM HEPES NA, PH7.5, 5% V/V PEG3350 WERE SOAKED REMARK 280 OVERNIGHT WITH 2.5MM EF4195 IN 50MM HEPES NA, PH7.5, 10% V/V REMARK 280 PEG3350, 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 27.01700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.25850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.25850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.01700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.07800 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 GLU A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 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 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 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 6 CG CD CE NZ REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 24 CG CD CE NZ REMARK 470 ARG A 50 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 ARG A 150 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 LYS A 278 CG CD CE NZ 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 LYS A 6 46.37 31.52 REMARK 500 GLU A 73 -149.64 54.99 REMARK 500 ASN A 74 43.92 -89.88 REMARK 500 ARG A 126 -17.98 78.26 REMARK 500 ASN A 132 13.00 54.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SA0 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 10 HET EDO A 302 10 HET EDO A 303 10 HET EDO A 304 10 HET 8KQ A 305 43 HET 8KQ A 306 43 HETNAM EDO 1,2-ETHANEDIOL HETNAM 8KQ 2-{[(3R)-2,3,4,9-TETRAHYDRO-1H-CARBAZOL-3-YL]AMINO}-5- HETNAM 2 8KQ (TRIFLUOROMETHYL)BENZOIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 8KQ 2(C20 H17 F3 N2 O2) FORMUL 8 HOH *95(H2 O) HELIX 1 AA1 SER A 46 GLU A 57 1 12 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 ALA A 170 LEU A 175 1 6 HELIX 5 AA5 THR A 182 ARG A 199 1 18 HELIX 6 AA6 SER A 207 GLY A 220 1 14 HELIX 7 AA7 GLY A 229 MET A 233 5 5 HELIX 8 AA8 ASP A 247 VAL A 251 5 5 HELIX 9 AA9 ASP A 256 LEU A 267 1 12 HELIX 10 AB1 SER A 276 ALA A 282 1 7 HELIX 11 AB2 HIS A 283 GLN A 287 5 5 SHEET 1 AA1 5 PHE A 4 GLY A 11 0 SHEET 2 AA1 5 GLY A 16 ASN A 23 -1 O LYS A 20 N GLU A 8 SHEET 3 AA1 5 VAL A 29 ILE A 35 -1 O LEU A 32 N TYR A 19 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 THR A 72 -1 N LEU A 67 O VAL A 79 SHEET 1 AA2 3 GLN A 85 ASP A 86 0 SHEET 2 AA2 3 LEU A 134 ILE A 135 -1 O ILE A 135 N GLN A 85 SHEET 3 AA2 3 ILE A 141 LYS A 142 -1 O LYS A 142 N LEU A 134 CISPEP 1 PRO A 253 PRO A 254 0 3.35 CRYST1 54.034 72.156 72.517 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 0.018507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013790 0.00000