SMTL ID : 9o0r.2 (1 other biounit)

Crystal structure of wild-type KRAS (GDP-bound) in complex with MRTX849 (adagrasib)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: ZN.2, 01.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:D.31, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:K.17, A:K.17, A:S.18, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.1 ZN.5: 4 residues within 4Å: Chain A: H.96, E.99, Q.100 Ligands: ACT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.96, A:E.99, ACT.4 ZN.6: 2 residues within 4Å: Chain A: E.4, D.55 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.4, A:D.55, H2O.1, H2O.3

1 x 01: Adagrasib

01.3: 23 residues within 4Å: Chain A: V.10, G.11, G.13, K.17, P.35, T.59, A.60, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.1, ACT.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.10, A:P.35, A:Y.65, A:R.69, A:M.73, A:H.96, A:Q.100, A:I.101, A:V.104, A:V.104 Hydrogen bonds: A:G.11, A:K.17, A:Y.65 Salt bridges: A:E.63

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: H.96, E.99, Q.100 Ligands: 01.3, ZN.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.100 Salt bridges: A:H.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alexander, P. et al., Biophysical and structural analysis of KRAS switch-II pocket inhibitors reveals allele-specific binding constraints. J.Biol.Chem. (2025)

Release Date

2025-06-25

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase KRas

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