SMTL ID : 9bi1.1

Crystal structure of GMPPNP bound KRAS G12D in complex with CYPA and RMC-7977

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 27 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:V.30, A:D.31, A:Y.33, A:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:D.34, A:Q.62, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GNP.5: 27 residues within 4Å: Chain D: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, E.32, Y.33, D.34, P.35, T.36, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:A.12, D:G.14, D:V.15, D:G.16, D:K.17, D:K.17, D:S.18, D:A.19, D:D.31, D:T.36, D:G.61, D:N.117, D:K.118, D:K.118, D:S.146, D:A.147, D:K.148 Water bridges: D:D.34 Salt bridges: D:D.120 pi-Stacking: D:F.29, D:F.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.17, S.18, T.36 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain D: K.17, S.18, P.35, T.36 Ligands: GNP.5 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.18, D:T.36, H2O.21, H2O.21

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.3: 32 residues within 4Å: Chain A: Y.33, D.34, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68 Chain B: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, G.75, A.102, N.103, A.104, Q.112, F.114, E.121, W.122, L.123, H.127, R.149, N.150 Chain D: G.1, E.4, R.42 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.58, B:F.61, B:F.61, B:F.114, B:W.122, B:W.122, B:L.123, A:P.35, A:I.37, A:A.60, A:Q.62, A:Y.65 Hydrogen bonds: B:R.56, B:Q.64, B:N.103, B:N.103 Water bridges: B:R.56, B:A.104, B:R.149 Salt bridges: B:R.56 pi-Stacking: A:Y.65, A:Y.65 ZNI.4: 32 residues within 4Å: Chain A: G.1, R.42 Chain C: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, G.75, A.102, N.103, A.104, Q.112, F.114, T.120, E.121, W.122, L.123, H.127, R.149, N.150 Chain D: Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, Y.72 23 PLIP interactions: 9 interactions with chain D, 14 interactions with chain C Hydrophobic interactions: D:P.35, D:I.37, D:I.37, D:A.60, D:Q.62, D:Y.65, D:Y.65, D:Y.65, C:I.58, C:I.58, C:F.61, C:F.61, C:F.114, C:W.122, C:L.123 pi-Stacking: D:Y.65 Hydrogen bonds: C:R.56, C:Q.64, C:N.103, C:N.103 Water bridges: C:R.56 Salt bridges: C:R.56 pi-Cation interactions: C:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuevas-Navarro, A. et al., Pharmacological restoration of GTP hydrolysis by mutant RAS. Nature (2025)

Release Date

2024-11-06

Peptides

GTPase KRas: AD
Peptidyl-prolyl cis-trans isomerase A: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

C
D

GTPase KRas

Peptidyl-prolyl cis-trans isomerase A

Related Entries With Identical Sequence