SMTL ID : 9baj.4 (3 other biounits)

Crystal structure of GDP-bound human K-RAS in a covalent complex with aryl sulfonyl fluoride compounds.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.17, Y.32, P.34, D.57 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.2, H2O.2, H2O.2, H2O.3

1 x 01: 3-(dioxo-lambda~6~-sulfanyl)-N-phenylbenzene-1-sulfonamide

01.2: 11 residues within 4Å: Chain A: E.3, K.5, L.6, V.7, S.39, D.54, I.55, L.56, Y.71, T.74, G.75 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.5, A:V.7, A:D.54, A:L.56, A:Y.71, A:Y.71 pi-Stacking: A:Y.71

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

GDP.3: 22 residues within 4Å: Chain A: A.11, G.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, P.34, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.1 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:D.30, A:E.31, A:E.31, A:Y.32, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:S.17, A:S.17, A:S.17, A:S.17, A:Y.32, A:P.34, A:T.58 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Landgraf, A. et al., Small-Molecule KRAS Inhibitors by Tyrosine Covalent Bond Formation. Chemmedchem (2025)

Release Date

2025-04-09

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Isoform 2B of GTPase KRas

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