SMTL ID : 7mdp.1

KRas G12C in complex with G-2897

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x Z07: 4-(trifluoromethyl)-1,3-benzothiazol-2-amine(Non-covalent)

Z07.1: 12 residues within 4Å: Chain A: V.9, E.62, E.63, Y.64, R.68, D.69, M.72, Y.96, Q.99, I.100, R.102, V.103 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.9, A:Y.96, A:Q.99, A:I.100 Hydrogen bonds: A:D.69, A:D.69, A:R.102

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Covalent)

GDP.2: 18 residues within 4Å: Chain A: A.11, G.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, E.31, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:D.30, A:E.31, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17 Salt bridges: A:K.16, A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.17 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.1, H2O.1

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: I.21, Q.25, V.29, Y.32 Chain B: S.28 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.21, A:V.29, A:Y.32 Hydrogen bonds: A:Q.25, B:S.28 ACT.11: 6 residues within 4Å: Chain B: H.173, P.176 Chain C: S.168, K.169, Q.170, A.176 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.173

4 x CAD: CACODYLIC ACID(Non-covalent)

CAD.5: 5 residues within 4Å: Chain B: S.66, R.67, V.68, T.69, S.84 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.69, B:S.84 CAD.6: 6 residues within 4Å: Chain B: W.34, E.51, N.59, S.100 Chain C: W.91, W.98 No protein-ligand interaction detected (PLIP) CAD.7: 4 residues within 4Å: Chain B: L.106, D.110, Y.111 Chain C: P.55 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.110 Water bridges: C:L.46 CAD.16: 9 residues within 4Å: Chain B: G.43, K.44 Chain C: P.7, D.85, Y.87, G.102, G.103, T.104, K.105 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.103, C:K.105

4 x P15: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL(Non-covalent)

P15.8: 5 residues within 4Å: Chain B: Q.3, L.4, Q.5, A.23, S.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.25 P15.10: 10 residues within 4Å: Chain B: V.93, Y.95, Q.114, G.115, L.117 Chain C: Q.38, L.39, P.40, G.41, D.85 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:L.117 Hydrogen bonds: C:G.41 P15.12: 2 residues within 4Å: Chain B: N.208, K.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.208, B:K.215 P15.18: 6 residues within 4Å: Chain C: Q.37, K.45, L.46, S.56, G.57, P.59 No protein-ligand interaction detected (PLIP)

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 2 residues within 4Å: Chain B: T.58, N.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.59 Water bridges: B:T.58 EDO.13: 2 residues within 4Å: Chain B: R.39, L.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.39 EDO.14: 5 residues within 4Å: Chain C: S.30, N.31, Y.32, N.51, K.66 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.30, C:N.51, C:K.66 EDO.15: 4 residues within 4Å: Chain B: V.178, L.179 Chain C: E.163, T.164 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:L.179, C:E.163, C:T.164, C:T.164

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.17: 3 residues within 4Å: Chain C: S.8, A.9, S.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, C.W. et al., Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors. Nat.Biotechnol. (2022)

Release Date

2022-03-16

Peptides

Isoform 2B of GTPase KRas: A
IgG heavy chain: B
IgG light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
I

Isoform 2B of GTPase KRas

IgG heavy chain

IgG light chain

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