SMTL ID : 9ct8.2 (1 other biounit)

Tricomplex of Compound 2, KRAS G12D, and CypA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

hetero-1-1-mer

Ligands

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

GNP.1: 25 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, 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 26 PLIP interactions: 26 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:S.18, A:A.19, A:V.30, A:Y.33, 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: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.2

1 x 01: (2R)-2-amino-N-(2-{[(1R)-1-cyclopentyl-2-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-2-oxoethyl](methyl)amino}-2-oxoethyl)-N-methylpropanamide (non-preferred name)

01.3: 28 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, G.73, T.74, G.75, A.102, N.103, A.104, Q.112, F.114, L.123, H.127, R.149 Ligands: CL.4 26 PLIP interactions: 8 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:D.13, A:I.37, A:A.60, A:Q.62, A:Y.65, A:M.68, B:I.58, B:I.58, B:F.61, B:F.61, B:A.102, B:Q.112, B:F.114, B:L.123, B:R.149 Water bridges: A:T.36 pi-Stacking: A:Y.65 Hydrogen bonds: B:R.56, B:R.56, B:Q.64, B:Q.64, B:N.103, B:N.103, B:A.104 Salt bridges: B:R.56 pi-Cation interactions: B:R.56

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

CL.4: 2 residues within 4Å: Chain A: Y.65 Ligands: 01.3 Ligand excluded by PLIP

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
B

B
C

Isoform 2B of GTPase KRas

Peptidyl-prolyl cis-trans isomerase A

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