SMTL ID : 7rp3.1

Crystal structure of GNE-1952 alkylated KRAS G12C in complex with 2H11 CLAMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MKZ: 1-[4-[6-chloranyl-7-(5-methyl-1~{H}-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl]propan-1-one(Covalent)

MKZ.1: 21 residues within 4Å: Chain A: G.12, C.14, K.18, P.36, T.60, A.61, G.62, Q.63, E.64, E.65, Y.66, R.70, D.71, M.74, H.97, Y.98, Q.101, I.102, R.104, V.105 Ligands: GDP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.36, A:Y.66, A:M.74, A:Y.98, A:Y.98, A:Q.101, A:V.105 Hydrogen bonds: A:K.18, A:D.71, A:D.71, A:R.104

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 22 residues within 4Å: Chain A: A.13, C.14, G.15, V.16, G.17, K.18, S.19, A.20, F.30, V.31, D.32, E.33, Y.34, N.118, K.119, D.121, L.122, S.147, A.148, K.149 Ligands: MKZ.1, MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.15, A:V.16, A:G.17, A:K.18, A:S.19, A:A.20, A:V.31, A:N.118, A:K.119, A:A.148, A:K.149 Water bridges: A:K.18, A:K.18, A:S.19, A:S.19, A:S.19, A:S.19, A:Y.34, A:Y.34, A:P.36 Salt bridges: A:K.18, A:D.121 pi-Stacking: A:F.30, A:F.30

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.19 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.19, H2O.1, H2O.1, H2O.1, H2O.1

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: E.39, L.58, Y.73 Chain B: S.101, W.103 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.39, A:E.39, B:R.98, B:S.101, B:S.101 Water bridges: A:E.39, A:D.40, A:S.41, A:S.41, A:S.41 GOL.5: 3 residues within 4Å: Chain A: E.64, D.94, H.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.64 Water bridges: A:D.94, A:Y.98 GOL.6: 5 residues within 4Å: Chain A: S.67, A.68, M.69 Chain C: S.56, G.57 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.68, A:M.69, C:G.57 GOL.11: 8 residues within 4Å: Chain C: Q.37, K.45, L.47, G.57, V.58, F.62, E.81, D.82 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.37, C:K.45, C:D.82, C:D.82 Water bridges: C:Q.37, C:K.45

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

EDO.7: 3 residues within 4Å: Chain A: Y.73 Chain B: D.110, Y.111 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:L.46 Hydrogen bonds: B:D.110 EDO.8: 3 residues within 4Å: Chain B: S.181 Chain C: A.160, G.161 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.181, B:S.181, C:G.161 Water bridges: C:E.163 EDO.10: 5 residues within 4Å: Chain A: A.68, M.69, Q.72 Chain C: Y.49, R.54 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.49, A:Q.72 Water bridges: C:Q.53, C:Q.53

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain C: E.83, V.108, G.110, Q.111, Y.143 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.108, C:G.110, C:Q.111 Water bridges: C:Y.175

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
immunoglobulin IgG heavy chain: B
immunoglobulin IgG light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
I

Isoform 2B of GTPase KRas

immunoglobulin IgG heavy chain

immunoglobulin IgG light chain

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