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(-) Description

Title :  CRYSTAL STRUCTURE OF SMALL MOLECULE VINYLSULFONAMIDE 9 COVALENTLY BOUND TO K-RAS G12C
 
Authors :  J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
Date :  31 Jul 13  (Deposition) - 27 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Gtpase, Gdp Bound, Small Molecule Inhibitor, Covalent Binder, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Ostrem, U. Peters, M. L. Sos, J. A. Wells, K. M. Shokat
K-Ras(G12C) Inhibitors Allosterically Control Gtp Affinity And Effector Interactions.
Nature V. 503 548 2013
PubMed-ID: 24256730  |  Reference-DOI: 10.1038/NATURE12796

(-) Compounds

Molecule 1 - GTPASE KRAS
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPJEXPRESS411
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-169
    GeneKRAS, KRAS ISOFORM 2B, KRAS2, RASK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymK-RAS 2, KI-RAS, C-K-RAS, C-KI-RAS, GTPASE KRAS, N- TERMINALLY PROCESSED

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (1x)A  
Biological Unit 3 (1x) B 
Biological Unit 4 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
121F2Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
121F2Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
121F-1Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
121F1Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
121F1Ligand/IonN-{1-[N-(4-CHLORO-5-IODO-2-METHOXYPHENYL)GLYCYL]PIPERIDIN-4-YL}ETHANESULFONAMIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:64 , SER A:65 , ALA A:66 , MET A:67 , HOH A:414BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREGLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , HOH A:318 , HOH A:326 , HOH A:338 , HOH A:349 , HOH A:350 , HOH A:370 , HOH A:409 , HOH A:426 , HOH A:440 , HOH A:447BINDING SITE FOR RESIDUE GDP A 202
3AC3SOFTWAREVAL B:9 , GLY B:10 , CYS B:12 , THR B:58 , GLU B:62 , ARG B:68 , TYR B:71 , MET B:72 , TYR B:96 , GLN B:99 , HOH B:312BINDING SITE FOR RESIDUE 21F B 201
4AC4SOFTWAREGLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , HOH B:303 , HOH B:318 , HOH B:329 , HOH B:340 , HOH B:353 , HOH B:355 , HOH B:394 , HOH B:396 , HOH B:410 , HOH B:411 , HOH B:417 , HOH B:420BINDING SITE FOR RESIDUE GDP B 202
5AC5SOFTWARELYS C:5 , LEU C:6 , VAL C:7 , ASP C:54 , LEU C:56 , HOH C:389BINDING SITE FOR RESIDUE SO4 C 201
6AC6SOFTWAREGLY C:10 , CYS C:12 , THR C:58 , ALA C:59 , GLY C:60 , TYR C:71 , MET C:72 , TYR C:96 , GLN C:99 , HOH C:386BINDING SITE FOR RESIDUE 21F C 202
7AC7SOFTWAREGLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , ALA C:59 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147 , HOH C:324 , HOH C:390 , HOH C:392BINDING SITE FOR RESIDUE GDP C 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LYH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LYH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LYH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LYH)

(-) Exons   (0, 0)

(no "Exon" information available for 4LYH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains d4lyha_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh.......eeeeeeee..eeeeeeeeee.....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyh A   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVDIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        30|       45        55        65        75        85        95       105       115       125       135       145       155       165   
                                                        30|                                                                                                                                    
                                                         36                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4lyhb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhh....eeeeee..eeeeeee........hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyh B   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK 169
                                    10        20        40        50        60        70        80        90       100       110       120       130       140       150       160         
                                                       29|                                                                                                                                 
                                                        40                                                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4lyhc_ C: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh....eeeeeee..eeeeeeeee....hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lyh C   1 MTEYKLVVVGACGVGKSALTIQLIQNHFVSYRKQVVIDGETSLLDILDTAGYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                    10        20        39        49        59||      72        82        92       102       112       122       132       142       152       162      
                                                       29|                   60|                                                                                                        
                                                        39                    64                                                                                                        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LYH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LYH)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RASK_HUMAN | P011161d8d 1d8e 1kzo 1kzp 1n4p 1n4q 1n4r 1n4s 3gft 4dsn 4dso 4dst 4dsu 4epr 4ept 4epv 4epw 4epx 4epy 4l8g 4ldj 4lpk 4lrw 4luc 4lv6 4lyf 4lyj 4m1o 4m1s 4m1t 4m1w 4m1y 4m21 4m22 4nmm 4obe 4pzy 4pzz 4q01 4q02 4q03 4ql3 4tq9 4tqa 4wa7 5f2e 5kyk 5tar 5tb5 5uqw 5us4 5usj 5v6s 5v6v 5xco

(-) Related Entries Specified in the PDB File

4l8g RELATED PROTEIN MUTANT
4l9s RELATED PROTEIN ISOFORM
4l9w RELATED PROTEIN ISOFORM
4lpk WILD-TYPE FORM OF PROTEIN
4lrw PROTEIN WITHOUT INHIBITOR BOUND
4luc PROTEIN BOUND TO RELATED COMPOUND
4lv6 PROTEIN BOUND TO RELATED COMPOUND
4lyf PROTEIN BOUND TO RELATED COMPOUND
4lyj RELATED COMPOUND BOUND TO PROTEIN
4m1o RELATED COMPOUND BOUND TO PROTEIN
4m1s RELATED COMPOUND BOUND TO PROTEIN
4m1t RELATED COMPOUND BOUND TO PROTEIN
4m1w RELATED COMPOUND BOUND TO PROTEIN
4m1y RELATED COMPOUND BOUND TO PROTEIN
4m21 RELATED COMPOUND BOUND TO PROTEIN
4m22 RELATED COMPOUND BOUND TO PROTEIN