SMTL ID : 9ctb.2 (1 other biounit)

Tri-complex of zoldonrasib (RMC-9805), 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: 25 residues within 4Å: Chain B: 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, 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 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:S.18, B:A.19, B:V.30, B:Y.33, B:T.36, B:T.36, B:G.61, 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.31, B:D.34 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GNP.1 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.10, H2O.10

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: L.123 Chain B: Y.65 Ligands: 01.4 Ligand excluded by PLIP

1 x 01: (2R)-2-cyclopentyl-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(2S,6R,8S,10R,14S,21M)-21-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-22-(2,2,2-trifluoroethyl)-5,16-dioxa-2,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),20,23,26-tetraen-8-yl]acetamide (non-preferred name)

01.4: 30 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: D.13, Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, R.69, Y.72 Ligands: CL.3 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.58, A:F.61, A:F.61, A:A.102, A:Q.112, A:F.114, A:W.122, A:L.123, B:D.13, B:P.35, B:I.37, B:A.60, B:Y.65 Hydrogen bonds: A:R.56, A:R.56, A:Q.64, A:Q.64, A:N.103, A:N.103 Water bridges: A:R.149 Salt bridges: A:R.56 pi-Stacking: B:Y.65

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Peptidyl-prolyl cis-trans isomerase A

Isoform 2B of GTPase KRas

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