SMTL ID : 9e9h.1

Crystal structure of human KRAS G12C covalently bound to DEL triazine compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: S.31 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.31, H2O.1, H2O.1, H2O.1, H2O.2

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

GDP.2: 20 residues within 4Å: Chain A: A.25, C.26, G.27, V.28, G.29, K.30, S.31, A.32, F.42, V.43, D.44, N.130, K.131, D.133, L.134, S.159, A.160, K.161 Ligands: CA.1, 01.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.27, A:V.28, A:G.29, A:K.30, A:S.31, A:A.32, A:D.44, A:N.130, A:K.131, A:K.131, A:A.160, A:K.161 Water bridges: A:S.31, A:S.31, A:Y.46 Salt bridges: A:K.30, A:D.133 pi-Stacking: A:F.42, A:F.42

1 x 01: (3S)-N,5-dimethyl-3-({4-[3-(morpholin-4-yl)phenyl]-6-(2-propanoyl-2,6-diazaspiro[3.4]octan-6-yl)-1,3,5-triazin-2-yl}amino)hexanamide

01.3: 19 residues within 4Å: Chain A: V.23, G.24, C.26, K.30, P.48, T.72, A.73, G.74, E.77, Y.78, S.79, R.82, D.83, M.86, D.106, H.109, Y.110, Q.113 Ligands: GDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.23, A:Y.110 Hydrogen bonds: A:K.30, A:S.79, A:R.82, A:Y.110, A:Q.113, A:Q.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, D. et al., Identification of Structurally Novel KRAS G12C Inhibitors through Covalent DNA-Encoded Library Screening. J.Med.Chem. (2025)

Release Date

2025-02-26

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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