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(-) Description

Title :  COVALENT GTP-COMPETITIVE INHIBITORS OF KRAS G12C: GUANOSINE BISPHOSPHONATE ANALOGS
 
Authors :  Y. Xiong, J. Lu, J. Hunter, L. Li, D. Scott, A. Manandhar, S. Gondi, K. D. W N. S. Gray
Date :  21 Jul 16  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Kras, Cancer, Covalent Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xiong, J. Lu, J. Hunter, L. Li, D. Scott, H. G. Choi, S. M. Lim, A. Manandhar, S. Gondi, T. Sim, K. D. Westover, N. S. Gray
Covalent Guanosine Mimetic Inhibitors Of G12C Kras.
Acs Med Chem Lett V. 8 61 2017
PubMed-ID: 28105276  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00373

(-) Compounds

Molecule 1 - GTPASE KRAS
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-168
    Gene: KRAS, KRAS2, RASK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
16ZD3Ligand/Ion5'-O-[(R)-[({2-[(CHLOROACETYL)AMINO]ETHYL}SULFAMOYL)METHYL](HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16ZD1Ligand/Ion5'-O-[(R)-[({2-[(CHLOROACETYL)AMINO]ETHYL}SULFAMOYL)METHYL](HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16ZD1Ligand/Ion5'-O-[(R)-[({2-[(CHLOROACETYL)AMINO]ETHYL}SULFAMOYL)METHYL](HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
16ZD1Ligand/Ion5'-O-[(R)-[({2-[(CHLOROACETYL)AMINO]ETHYL}SULFAMOYL)METHYL](HYDROXY)PHOSPHORYL]GUANOSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLY A:13 , GLY A:15 , 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:147binding site for residue 6ZD A 201
2AC2SOFTWAREALA B:11 , GLY B:13 , VAL B:14 , GLY B:15 , ALA B:18 , PHE B:28 , VAL B:29 , ASP B:30 , GLU B:31 , THR B:58 , GLN B:61 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , ALA B:146 , LYS B:147 , HOH B:305binding site for Di-peptide 6ZD B 201 and CYS B 12
3AC3SOFTWARECYS B:12 , GLY B:13 , GLY B:15 , ALA B:18 , PHE B:28 , VAL B:29 , ASP B:30 , GLU B:31 , THR B:58 , ASN B:116 , LYS B:117 , CYS B:118 , LEU B:120 , PRO B:121 , SER B:145 , ALA B:146 , LYS B:147 , HOH B:305binding site for Di-peptide 6ZD B 201 and ASP B 119
4AC4SOFTWARECYS B:12 , GLY B:13 , GLY B:15 , ALA B:18 , GLN B:22 , PHE B:28 , VAL B:29 , ASP B:30 , GLU B:31 , THR B:58 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:145 , LYS B:147 , THR B:148 , HOH B:305binding site for Di-peptide 6ZD B 201 and ALA B 146
5AC5SOFTWARECYS C:12 , GLY C:13 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , VAL C:29 , ASP C:30 , PRO C:34 , ALA C:59 , ASN C:116 , LYS C:117 , CYS C:118 , LEU C:120 , PRO C:121 , SER C:145 , ALA C:146 , LYS C:147binding site for Di-peptide 6ZD C 201 and ASP C 119
6AC6SOFTWARECYS C:12 , GLY C:13 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , GLN C:22 , PHE C:28 , VAL C:29 , ASP C:30 , PRO C:34 , ALA C:59 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , LYS C:147 , THR C:148binding site for Di-peptide 6ZD C 201 and ALA C 146
7AC7SOFTWAREALA C:11 , GLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , VAL C:29 , ASP C:30 , PRO C:34 , ALA C:59 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147binding site for Di-peptide 6ZD C 201 and CYS C 12

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KYK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KYK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KYK)

(-) Exons   (0, 0)

(no "Exon" information available for 5KYK)

(-) 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:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhh........eeeeeeee..eeeeeeeee......hhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kyk A   0 GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDDSYRKQVVIDGETCLLDILDTAGQERDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK 167
                                     9        19        29   ||   43        53        68        78        88        98       108       118       128       138       148       158         
                                                            33|                      62|                                                                                                   
                                                             38                       68                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhh........eeeeeeee..eeeeeeeee......hhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kyk B   0 GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDDSYRKQVVIDGETCLLDILDTAGQERDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                     9        19        29   ||   43        53        68        78        88        98       108       118       128       138       148       158       168
                                                            33|                      62|                                                                                                    
                                                             38                       68                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhh.........eeeeeeee..eeeeeeeee.......hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kyk C   0 GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPDSYRKQVVIDGETCLLDILDTAGQESAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE 168
                                     9        19        29    ||  42        52        62|       74        84        94       104       114       124       134       144       154       164    
                                                             34|                      62|                                                                                                       
                                                              38                       65
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5KYK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KYK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KYK)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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  5kyk
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  RASK_HUMAN | P01116
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 Related Entries

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

UniProtKB/Swiss-Prot
        RASK_HUMAN | P01116: 1d8d 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 4lyh 4lyj 4m1o 4m1s 4m1t 4m1w 4m1y 4m21 4m22 4nmm 4obe 4pzy 4pzz 4q01 4q02 4q03 4ql3 4tq9 4tqa 4wa7 5f2e 5tar 5tb5 5uqw 5us4 5usj 5v6s 5v6v 5xco

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