SMTL ID : 9cta.1 (1 other biounit)

Tricomplex of RMC-9945, KRAS G12D, and CypA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 24 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, Y.33, P.35, T.36, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: 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:T.36, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:D.31, A:D.31, A:D.34, A:T.36 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: 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.1

1 x 01: (2R)-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-21-(2,2,2-trifluoroethyl)-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-methylbutanamide (non-preferred name)

01.3: 26 residues within 4Å: Chain A: D.13, Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, Y.72 Chain B: R.56, I.58, F.61, M.62, Q.64, A.102, N.103, A.104, Q.112, F.114, E.121, W.122, L.123, H.127, R.149 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.58, B:F.61, B:F.61, B:A.102, B:Q.112, B:F.114, B:W.122, B:L.123, A:P.35, A:I.37, A:A.60, A:Y.65 Hydrogen bonds: B:R.56, B:Q.64, B:Q.64, B:N.103, B:N.103 Water bridges: B:R.56 Salt bridges: B:R.56 pi-Stacking: A:Y.65 Halogen bonds: A:Q.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weller, C. et al., A neomorphic protein interface catalyzes covalent inhibition of RAS G12D aspartic acid in tumors. Science (2025)

Release Date

2025-07-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Isoform 2B of GTPase KRas

Peptidyl-prolyl cis-trans isomerase A

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