HEADER HYDROLASE/HYDROLASE INHIBITOR 17-MAR-17 5V6V TITLE CRYSTAL STRUCTURE OF SMALL MOLECULE AZIRIDINE 3 COVALENTLY BOUND TO K- TITLE 2 RAS G12C COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS K-RAS G12C, COVALENT INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.M.MCGREGOR,M.JENKINS,C.KERWIN,J.E.BURKE,K.M.SHOKAT REVDAT 4 20-NOV-19 5V6V 1 REMARK REVDAT 3 20-SEP-17 5V6V 1 REMARK REVDAT 2 05-JUL-17 5V6V 1 JRNL REVDAT 1 28-JUN-17 5V6V 0 JRNL AUTH L.M.MCGREGOR,M.L.JENKINS,C.KERWIN,J.E.BURKE,K.M.SHOKAT JRNL TITL EXPANDING THE SCOPE OF ELECTROPHILES CAPABLE OF TARGETING JRNL TITL 2 K-RAS ONCOGENES. JRNL REF BIOCHEMISTRY V. 56 3178 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28621541 JRNL DOI 10.1021/ACS.BIOCHEM.7B00271 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 30189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 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 37.4403 - 3.8240 0.98 2653 150 0.1615 0.1926 REMARK 3 2 3.8240 - 3.0357 0.96 2616 144 0.1611 0.1776 REMARK 3 3 3.0357 - 2.6521 0.97 2631 157 0.1677 0.1891 REMARK 3 4 2.6521 - 2.4096 0.96 2598 148 0.1606 0.1973 REMARK 3 5 2.4096 - 2.2369 0.96 2604 138 0.1516 0.1763 REMARK 3 6 2.2369 - 2.1051 0.96 2626 133 0.1588 0.2336 REMARK 3 7 2.1051 - 1.9997 0.95 2606 125 0.1661 0.2036 REMARK 3 8 1.9997 - 1.9126 0.95 2614 138 0.1768 0.2453 REMARK 3 9 1.9126 - 1.8390 0.95 2553 116 0.1972 0.2483 REMARK 3 10 1.8390 - 1.7755 0.95 2597 144 0.2177 0.2536 REMARK 3 11 1.7755 - 1.7200 0.94 2551 147 0.2370 0.3067 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) : 22.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.19 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 : 0.011 2881 REMARK 3 ANGLE : 0.975 3880 REMARK 3 CHIRALITY : 0.052 424 REMARK 3 PLANARITY : 0.006 488 REMARK 3 DIHEDRAL : 13.029 1683 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 5V6V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30203 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 60.493 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : 0.32100 REMARK 200 FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 4000, 0.1M TRIS PH 8, 0.2M REMARK 280 CACL2, VAPOR DIFFUSION, HANGING DROP, 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 0 REMARK 465 MET A 1 REMARK 465 GLU A 168 REMARK 465 LYS A 169 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 LYS B 169 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 B 31 CG CD OE1 OE2 REMARK 470 ARG B 41 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS B 12 H262 8YA B 207 1.14 REMARK 500 O HOH A 331 O HOH A 435 1.87 REMARK 500 O HOH A 334 O HOH A 347 2.00 REMARK 500 O HOH A 434 O HOH A 437 2.02 REMARK 500 O HOH A 432 O HOH A 437 2.10 REMARK 500 O HOH A 306 O HOH A 342 2.11 REMARK 500 O HOH A 327 O HOH A 388 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 334 O HOH B 316 1556 1.91 REMARK 500 OE1 GLU A 3 NZ LYS B 147 1556 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 33 111.62 -39.39 REMARK 500 SER A 122 41.23 -96.32 REMARK 500 LYS B 117 36.85 70.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 201 O2B 87.7 REMARK 620 3 HOH A 348 O 90.9 87.8 REMARK 620 4 HOH A 319 O 78.5 89.1 169.1 REMARK 620 5 HOH A 430 O 170.9 96.4 97.3 93.4 REMARK 620 6 HOH A 340 O 88.4 168.3 81.2 101.0 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 138 O REMARK 620 2 HOH A 443 O 93.6 REMARK 620 3 HOH A 380 O 175.6 84.9 REMARK 620 4 HOH A 397 O 88.9 74.7 86.7 REMARK 620 5 HOH A 318 O 82.2 82.0 101.6 154.5 REMARK 620 6 GLU A 63 OE1 76.3 30.2 100.5 50.7 103.8 REMARK 620 7 GLU A 63 OE2 76.9 26.9 100.2 54.2 100.3 3.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 205 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 3 O REMARK 620 2 GLU B 76 OE1 93.3 REMARK 620 3 GLU B 76 OE2 117.8 53.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 OG REMARK 620 2 GDP B 202 O1B 89.2 REMARK 620 3 HOH B 319 O 175.7 87.0 REMARK 620 4 HOH B 327 O 91.1 86.6 90.7 REMARK 620 5 HOH B 318 O 81.4 92.0 96.7 172.4 REMARK 620 6 HOH B 326 O 87.2 170.6 96.9 84.8 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 138 O REMARK 620 2 HOH B 401 O 95.0 REMARK 620 3 HOH B 358 O 80.6 77.5 REMARK 620 4 GLU B 63 OE1 79.7 34.5 44.7 REMARK 620 5 GLU B 63 OE2 79.0 31.5 48.4 3.8 REMARK 620 6 HOH B 310 O 80.0 83.1 151.1 110.4 106.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 350 O REMARK 620 2 HOH A 388 O 67.9 REMARK 620 3 ASP B 108 OD1 18.5 86.4 REMARK 620 4 HOH B 400 O 125.1 60.1 142.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8YA A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 8YA B 207 and CYS B REMARK 800 12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V6S RELATED DB: PDB DBREF 5V6V A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 5V6V B 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 5V6V GLY A 0 UNP P01116 EXPRESSION TAG SEQADV 5V6V CYS A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5V6V SER A 51 UNP P01116 CYS 51 ENGINEERED MUTATION SEQADV 5V6V LEU A 80 UNP P01116 CYS 80 ENGINEERED MUTATION SEQADV 5V6V SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQADV 5V6V GLY B 0 UNP P01116 EXPRESSION TAG SEQADV 5V6V CYS B 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5V6V SER B 51 UNP P01116 CYS 51 ENGINEERED MUTATION SEQADV 5V6V LEU B 80 UNP P01116 CYS 80 ENGINEERED MUTATION SEQADV 5V6V SER B 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQRES 1 A 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA CYS SEQRES 2 A 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 A 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR SER SEQRES 5 A 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 A 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 170 PHE LEU LEU VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 A 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 A 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 A 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 A 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 A 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 A 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 A 170 LYS SEQRES 1 B 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA CYS SEQRES 2 B 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 B 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 B 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR SER SEQRES 5 B 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 B 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 B 170 PHE LEU LEU VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 B 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 B 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 B 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 B 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 B 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 B 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 B 170 LYS HET GDP A 201 39 HET CA A 202 1 HET CA A 203 1 HET 8YA A 204 55 HET CA B 201 1 HET GDP B 202 39 HET CA B 203 1 HET CA B 204 1 HET CA B 205 1 HET GOL B 206 14 HET 8YA B 207 55 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM CA CALCIUM ION HETNAM 8YA 3-AMINO-1-{4-[6-CHLORO-8-FLUORO-7-(5-METHYL-1H-INDAZOL- HETNAM 2 8YA 4-YL)QUINAZOLIN-4-YL]PIPERAZIN-1-YL}PROPAN-1-ONE HETNAM GOL GLYCEROL HETSYN 8YA KRAS(G12C) INHIBITOR, AZIRIDINE FORM, BOUND FORM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 CA 6(CA 2+) FORMUL 6 8YA 2(C23 H23 CL F N7 O) FORMUL 12 GOL C3 H8 O3 FORMUL 14 HOH *282(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 THR A 74 1 10 HELIX 3 AA3 ASN A 86 LYS A 104 1 19 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 HELIX 5 AA5 GLY A 151 LYS A 167 1 17 HELIX 6 AA6 GLY B 15 ASN B 26 1 12 HELIX 7 AA7 SER B 65 ARG B 73 1 9 HELIX 8 AA8 ASN B 86 ASP B 92 1 7 HELIX 9 AA9 ASP B 92 ASP B 105 1 14 HELIX 10 AB1 ASP B 126 GLY B 138 1 13 HELIX 11 AB2 GLY B 151 GLU B 168 1 18 SHEET 1 AA1 6 ASP A 38 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O ILE A 55 N TYR A 40 SHEET 3 AA1 6 GLU A 3 GLY A 10 1 N LEU A 6 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O VAL A 114 N LEU A 80 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SHEET 1 AA2 6 ASP B 38 ILE B 46 0 SHEET 2 AA2 6 GLU B 49 ASP B 57 -1 O ILE B 55 N TYR B 40 SHEET 3 AA2 6 GLU B 3 GLY B 10 1 N LEU B 6 O LEU B 56 SHEET 4 AA2 6 GLY B 77 ALA B 83 1 O VAL B 81 N VAL B 9 SHEET 5 AA2 6 MET B 111 ASN B 116 1 O VAL B 114 N LEU B 80 SHEET 6 AA2 6 PHE B 141 GLU B 143 1 O ILE B 142 N LEU B 113 LINK SG CYS A 12 C26 8YA A 204 1555 1555 1.76 LINK OG SER A 17 CA CA A 202 1555 1555 2.36 LINK O GLY A 138 CA CA A 203 1555 1555 2.22 LINK O GLU B 3 CA CA B 205 1555 1555 2.31 LINK SG CYS B 12 C26 8YA B 207 1555 1555 1.76 LINK OG SER B 17 CA CA B 203 1555 1555 2.34 LINK OE1 GLU B 76 CA CA B 205 1555 1555 2.39 LINK OE2 GLU B 76 CA CA B 205 1555 1555 2.45 LINK O GLY B 138 CA CA B 204 1555 1555 2.30 LINK O2B GDP A 201 CA CA A 202 1555 1555 2.28 LINK CA CA A 202 O HOH A 348 1555 1555 2.38 LINK CA CA A 202 O HOH A 319 1555 1555 2.39 LINK CA CA A 202 O HOH A 430 1555 1555 2.33 LINK CA CA A 202 O HOH A 340 1555 1555 2.37 LINK CA CA A 203 O HOH A 443 1555 1555 2.33 LINK CA CA A 203 O HOH A 380 1555 1555 2.30 LINK CA CA A 203 O HOH A 397 1555 1555 2.53 LINK CA CA A 203 O HOH A 318 1555 1555 2.36 LINK CA CA B 201 O HOH A 350 1555 1555 2.42 LINK CA CA B 201 O HOH A 388 1555 1555 2.46 LINK O1B GDP B 202 CA CA B 203 1555 1555 2.24 LINK CA CA B 203 O HOH B 319 1555 1555 2.31 LINK CA CA B 203 O HOH B 327 1555 1555 2.47 LINK CA CA B 203 O HOH B 318 1555 1555 2.44 LINK CA CA B 203 O HOH B 326 1555 1555 2.45 LINK CA CA B 204 O HOH B 401 1555 1555 2.43 LINK CA CA B 204 O HOH B 358 1555 1555 2.48 LINK OE1 GLU A 63 CA CA A 203 1555 1455 2.43 LINK OE2 GLU A 63 CA CA A 203 1555 1455 2.40 LINK OE1 GLU B 63 CA CA B 204 1555 1655 2.46 LINK OE2 GLU B 63 CA CA B 204 1555 1655 2.45 LINK OD1 ASP B 108 CA CA B 201 1555 1455 2.65 LINK CA CA B 201 O HOH B 400 1555 1655 2.50 LINK CA CA B 204 O HOH B 310 1555 1455 2.39 SITE 1 AC1 26 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 26 SER A 17 ALA A 18 PHE A 28 VAL A 29 SITE 3 AC1 26 ASP A 30 GLU A 31 ARG A 73 ASN A 116 SITE 4 AC1 26 LYS A 117 ASP A 119 LEU A 120 SER A 145 SITE 5 AC1 26 ALA A 146 LYS A 147 CA A 202 HOH A 303 SITE 6 AC1 26 HOH A 312 HOH A 314 HOH A 328 HOH A 348 SITE 7 AC1 26 HOH A 353 HOH A 370 SITE 1 AC2 6 SER A 17 GDP A 201 HOH A 319 HOH A 340 SITE 2 AC2 6 HOH A 348 HOH A 430 SITE 1 AC3 6 GLU A 63 GLY A 138 HOH A 318 HOH A 380 SITE 2 AC3 6 HOH A 397 HOH A 443 SITE 1 AC4 12 CYS A 12 ALA A 59 GLY A 60 TYR A 64 SITE 2 AC4 12 ARG A 68 ASP A 69 MET A 72 HIS A 95 SITE 3 AC4 12 TYR A 96 GLN A 99 VAL A 103 HOH A 320 SITE 1 AC5 4 HOH A 350 HOH A 388 ASP B 108 HOH B 400 SITE 1 AC6 24 GLY B 13 VAL B 14 GLY B 15 LYS B 16 SITE 2 AC6 24 SER B 17 ALA B 18 PHE B 28 VAL B 29 SITE 3 AC6 24 ASP B 30 ASN B 116 LYS B 117 ASP B 119 SITE 4 AC6 24 LEU B 120 SER B 145 ALA B 146 LYS B 147 SITE 5 AC6 24 CA B 203 HOH B 319 HOH B 327 HOH B 329 SITE 6 AC6 24 HOH B 338 HOH B 366 HOH B 372 HOH B 377 SITE 1 AC7 6 SER B 17 GDP B 202 HOH B 318 HOH B 319 SITE 2 AC7 6 HOH B 326 HOH B 327 SITE 1 AC8 5 GLU B 63 GLY B 138 HOH B 310 HOH B 358 SITE 2 AC8 5 HOH B 401 SITE 1 AC9 2 GLU B 3 GLU B 76 SITE 1 AD1 7 ILE A 21 GLN A 25 HIS A 27 TYR A 32 SITE 2 AD1 7 TYR A 40 GLN B 25 HOH B 379 SITE 1 AD2 12 ALA B 11 GLY B 13 VAL B 14 ALA B 59 SITE 2 AD2 12 GLY B 60 GLN B 61 TYR B 64 ARG B 68 SITE 3 AD2 12 ASP B 69 MET B 72 TYR B 96 GLN B 99 CRYST1 33.230 39.170 62.340 77.34 81.44 76.86 P 1 2 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 0.030093 -0.007025 -0.003238 0.00000 SCALE2 0.000000 0.026216 -0.005142 0.00000 SCALE3 0.000000 0.000000 0.016531 0.00000