SMTL ID : 9bhp.1

Crystal structure of KRAS G12C in a transition state mimetic complex with CYPA and RMC-7977

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZNI: (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide(Non-covalent)

ZNI.1: 28 residues within 4Å: Chain A: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, A.102, N.103, A.104, Q.112, F.114, E.121, W.122, L.123, H.127, R.149 Chain B: G.1, E.4, R.42 Chain D: Y.33, P.35, T.36, I.37, A.60, Q.62, Y.65, M.68 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:I.58, A:F.61, A:F.61, A:F.114, A:W.122, A:L.123, D:P.35, D:I.37, D:I.37, D:A.60, D:Y.65, D:Y.65, D:Y.65 Hydrogen bonds: A:R.56, A:Q.64, A:Q.64, A:N.103, A:N.103 Water bridges: A:R.56, A:R.149 Salt bridges: A:R.56 pi-Cation interactions: A:R.56 pi-Stacking: D:Y.65 ZNI.5: 25 residues within 4Å: Chain B: Y.33, P.35, T.36, I.37, A.60, Q.62, Y.65, M.68 Chain C: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, A.102, N.103, A.104, Q.112, F.114, E.121, W.122, L.123, H.127, R.149 19 PLIP interactions: 13 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:I.58, C:F.61, C:F.61, C:F.114, C:W.122, C:L.123, B:P.35, B:I.37, B:A.60, B:Y.65 Hydrogen bonds: C:R.56, C:Q.64, C:Q.64, C:N.103, C:N.103 Salt bridges: C:R.56 pi-Cation interactions: C:R.56 pi-Stacking: B:Y.65, B:Y.65

2 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.2: 12 residues within 4Å: Chain B: C.13, K.17, S.18, Y.33, P.35, T.36, T.59, A.60, G.61, Q.62 Ligands: GDP.3, MG.4 No protein-ligand interaction detected (PLIP) AF3.6: 13 residues within 4Å: Chain D: C.13, G.14, K.17, S.18, Y.33, P.35, T.36, T.59, A.60, G.61, Q.62 Ligands: GDP.7, MG.8 No protein-ligand interaction detected (PLIP)

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

GDP.3: 22 residues within 4Å: Chain B: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: AF3.2, MG.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:E.32, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:S.18, B:D.31, B:D.34, B:T.36 Salt bridges: B:K.17, B:D.120 pi-Stacking: B:F.29, B:F.29 GDP.7: 19 residues within 4Å: Chain D: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, S.146, A.147 Ligands: AF3.6, MG.8 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.14, D:V.15, D:G.16, D:K.17, D:S.18, D:A.19, D:V.30, D:N.117, D:K.118, D:A.147, D:K.148 Water bridges: D:S.18, D:S.18, D:T.36, D:T.36, D:Q.62 Salt bridges: D:K.17, D:D.120

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain B: S.18, T.36, D.58 Ligands: AF3.2, GDP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.3, H2O.4 MG.8: 5 residues within 4Å: Chain D: S.18, T.36, D.58 Ligands: AF3.6, GDP.7 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.18, D:T.36, H2O.9, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pourfarjam, Y. et al., Crystal structure of KRAS G12S in a transition state mimetic complex with CYPA and RMC-7977. To Be Published

Release Date

2024-11-06

Peptides

Peptidyl-prolyl cis-trans isomerase A: AC
Isoform 2B of GTPase KRas: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
B

B
A

D
C

Peptidyl-prolyl cis-trans isomerase A

Isoform 2B of GTPase KRas

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