SMTL ID : 9bg4.2 (1 other biounit)

Tri-complex of Compound-2, KRAS G12V, and CypA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

hetero-2-2-mer

Ligands

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

GNP.1: 24 residues within 4Å: Chain A: A.12, V.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:K.17, A:S.18, A:A.19, A:V.30, 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:S.18, A:D.34, A:T.36, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 GNP.4: 24 residues within 4Å: Chain B: A.12, V.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.5 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:K.17, B:S.18, B:A.19, B:V.30, B:Y.33, 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:S.18, B:D.31, B:D.31, B:D.34, B:T.36, B:Q.62 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

2 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.3 MG.5: 3 residues within 4Å: Chain B: S.18, T.36 Ligands: GNP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.18, B:T.36, H2O.11, H2O.12

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

CL.3: 2 residues within 4Å: Chain A: Y.65 Ligands: 01.8 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: Y.65 Ligands: 01.7 Ligand excluded by PLIP

2 x 01: (2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-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]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name)

01.7: 27 residues within 4Å: Chain A: Q.44 Chain B: Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, Y.72 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, L.123, H.127, R.149 Ligands: CL.6 23 PLIP interactions: 16 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:I.58, C:F.61, C:F.61, C:A.102, C:F.114, C:L.123, B:I.37, B:A.60, B:Q.62, B:Y.65, B:Y.65, B:M.68 Hydrogen bonds: C:R.56, C:R.56, C:Q.64, C:Q.64, C:N.103, C:N.103 Water bridges: C:R.149, C:R.149 Salt bridges: C:R.56 pi-Cation interactions: C:R.56 pi-Stacking: B:Y.65 01.8: 27 residues within 4Å: Chain A: Y.33, P.35, T.36, I.37, E.38, A.60, Q.62, Y.65, M.68, Y.72 Chain B: Q.44 Chain D: R.56, I.58, F.61, M.62, Q.64, G.73, T.74, A.102, N.103, A.104, Q.112, F.114, L.123, H.127, R.149 Ligands: CL.3 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:I.58, D:F.61, D:F.61, D:A.102, D:F.114, D:L.123, A:I.37, A:A.60, A:Q.62, A:Y.65 Hydrogen bonds: D:R.56, D:Q.64, D:Q.64, D:N.103, D:N.103 Water bridges: D:R.56, D:R.149 Salt bridges: D:R.56 pi-Cation interactions: D:R.56 pi-Stacking: A:Y.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cregg, J. et al., Discovery of Daraxonrasib (RMC-6236), a Potent and Orally Bioavailable RAS(ON) Multi-selective, Noncovalent Tri-complex Inhibitor for the Treatment of Patients with Multiple RAS-Addicted Cancers. J.Med.Chem. (2025)

Release Date

2025-03-19

Peptides

GTPase KRas: AB
Peptidyl-prolyl cis-trans isomerase A: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GTPase KRas

Peptidyl-prolyl cis-trans isomerase A

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