HEADER SIGNALING PROTEIN/INHIBITOR 04-DEC-19 6V5L TITLE THE HADDOCK STRUCTURE MODEL OF GDP KRAS IN COMPLEX WITH ITS ALLOSTERIC TITLE 2 INHIBITOR E22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 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: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KRAS, ALLOSTERIC INHIBITOR, DRUG DISCOVERY, HADDOCK, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX, SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.WANG,A.K.GUPTA,P.PRAKASH,J.P.PUTKEY,A.A.GORFE REVDAT 3 15-MAY-24 6V5L 1 REMARK REVDAT 2 14-JUN-23 6V5L 1 REMARK REVDAT 1 18-DEC-19 6V5L 0 JRNL AUTH A.K.GUPTA,X.WANG,C.V.PAGBA,P.PRAKASH,J.P.PUTKEY,A.A.GORFE JRNL TITL MULTI TARGET ENSEMBLE BASED VIRTUAL SCREENING YIELDS NOVEL JRNL TITL 2 ALLOSTERIC KRAS INHIBITORS AT HIGH SUCCESS RATE JRNL REF CHEMICAL BIOLOGY & DRUG V. 94 1441 2019 JRNL REF 2 DESIGN JRNL PMID 30903639 JRNL DOI 10.1111/CBDD REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, HADDOCK REMARK 3 AUTHORS : BONVIN (HADDOCK), BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6V5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245658. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 115; 115 REMARK 210 PRESSURE : 1 PA; 1 PA REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 KRAS, 1.0 MM E22, 5 MM [U-99% 2H] REMARK 210 DTT, 10 UM [U-99% 2H] DSS, 25 REMARK 210 MM NATURE ABUNDANCE SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 5 MM MAGNESIUM ION, 95% H2O/5% REMARK 210 D2O; 0.8 MM [U-99% 13C; U-99% REMARK 210 15N] KRAS, 1.0 MM E22, 5 MM [U- REMARK 210 99% 2H] DTT, 10 UM [U-99% 2H] REMARK 210 DSS, 25 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 5 MM REMARK 210 MAGNESIUM ION, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D NOESY 15N HSQC; 2D 15N REMARK 210 HSQC; 2D 13C HSQC; 3D CCH-TOCSY; REMARK 210 3D NOESY 13C HSQC; F1 13C 15N REMARK 210 FILTERED 3D NOESY 13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2, NMRPIPE, NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS 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 HZ3 LYS A 5 OD2 ASP A 54 1.57 REMARK 500 OD1 ASP A 33 HG1 THR A 35 1.57 REMARK 500 HH11 ARG A 41 OD1 ASP A 54 1.59 REMARK 500 OD2 ASP A 57 MG MG A 202 1.64 REMARK 500 OD1 ASP A 57 MG MG A 202 1.66 REMARK 500 OG SER A 17 MG MG A 202 1.69 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 1 LYS A 117 31.79 72.58 REMARK 500 2 PRO A 110 106.39 -56.75 REMARK 500 2 SER A 145 114.69 -161.41 REMARK 500 3 GLU A 37 79.49 -118.01 REMARK 500 4 ALA A 59 -63.92 -98.54 REMARK 500 4 PRO A 110 108.09 -59.84 REMARK 500 5 ALA A 59 -73.20 -86.76 REMARK 500 5 LYS A 117 41.27 71.39 REMARK 500 6 PRO A 110 107.52 -49.69 REMARK 500 7 PRO A 110 109.18 -53.98 REMARK 500 7 SER A 122 60.28 66.15 REMARK 500 7 GLN A 150 94.66 -69.83 REMARK 500 8 ASP A 105 70.81 55.73 REMARK 500 8 GLU A 107 -55.21 -125.41 REMARK 500 9 ILE A 24 -64.88 -104.30 REMARK 500 9 PRO A 110 104.23 -58.57 REMARK 500 10 ASP A 105 60.25 64.66 REMARK 500 10 PRO A 121 -169.81 -79.75 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 GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QPD A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30694 RELATED DB: BMRB REMARK 900 THE HADDOCK STRUCTURE MODEL OF GDP KRAS IN COMPLEX WITH ITS REMARK 900 ALLOSTERIC INHIBITOR E22 DBREF 6V5L A 1 169 UNP P01116 RASK_HUMAN 1 169 SEQRES 1 A 169 MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY GLY SEQRES 2 A 169 VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN ASN SEQRES 3 A 169 HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 A 169 TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS LEU SEQRES 5 A 169 LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SER SEQRES 6 A 169 ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY PHE SEQRES 7 A 169 LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE GLU SEQRES 8 A 169 ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL LYS SEQRES 9 A 169 ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN LYS SEQRES 10 A 169 CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN ALA SEQRES 11 A 169 GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE GLU SEQRES 12 A 169 THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA PHE SEQRES 13 A 169 TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU LYS HET GDP A 201 40 HET MG A 202 1 HET QPD A 203 39 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM QPD (2R)-2-[2-(1H-INDOLE-3-CARBONYL)HYDRAZINYL]-2- HETNAM 2 QPD PHENYLACETAMIDE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 QPD C17 H16 N4 O2 HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 TYR A 64 GLY A 75 1 12 HELIX 3 AA3 ASN A 86 ASP A 105 1 20 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 HELIX 5 AA5 GLY A 151 GLU A 168 1 18 SHEET 1 AA1 6 SER A 39 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O LEU A 53 N LYS A 42 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N TYR A 4 O ASP A 54 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 7 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O VAL A 114 N CYS A 80 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SITE 1 AC1 17 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 17 SER A 17 ALA A 18 PHE A 28 VAL A 29 SITE 3 AC1 17 ASP A 30 ASP A 57 ASN A 116 ASP A 119 SITE 4 AC1 17 LEU A 120 SER A 145 ALA A 146 LYS A 147 SITE 5 AC1 17 MG A 202 SITE 1 AC2 4 SER A 17 ASP A 57 THR A 58 GDP A 201 SITE 1 AC3 7 LYS A 5 LEU A 6 VAL A 7 ASP A 54 SITE 2 AC3 7 LEU A 56 GLN A 70 TYR A 71 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1