SMTL ID : 9e9i.1

Crystal Structure of human KRAS G12C covalently bound to nopinone-derived naphthol compound 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.32 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.32, H2O.1, H2O.1, H2O.2, H2O.4

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

GDP.2: 22 residues within 4Å: Chain A: A.26, C.27, G.28, V.29, G.30, K.31, S.32, A.33, F.43, V.44, D.45, Y.47, N.131, K.132, D.134, L.135, S.160, A.161, K.162 Ligands: MG.1, 01.3, EDO.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.28, A:V.29, A:G.30, A:K.31, A:S.32, A:A.33, A:V.44, A:Y.47, A:N.131, A:K.132, A:K.132, A:S.160, A:A.161, A:K.162 Salt bridges: A:K.31, A:D.134 pi-Stacking: A:F.43, A:F.43 pi-Cation interactions: A:K.132

1 x 01: 1-{6-[(4P,6R,8R)-3-fluoro-4-(3-hydroxynaphthalen-1-yl)-7,7-dimethyl-5,6,7,8-tetrahydro-6,8-methanoquinolin-2-yl]-2,6-diazaspiro[3.4]octan-2-yl}propan-1-one

01.3: 21 residues within 4Å: Chain A: G.25, C.27, K.31, P.49, T.73, A.74, G.75, Q.76, E.77, E.78, Y.79, S.80, R.83, D.84, M.87, H.110, Y.111, Q.114, I.115, V.118 Ligands: GDP.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.49, A:E.77, A:Y.79, A:Y.79, A:M.87, A:H.110, A:Y.111, A:Q.114, A:I.115, A:V.118 Hydrogen bonds: A:K.31, A:S.80, A:D.84, A:Q.114 Halogen bonds: A:R.83

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: K.20, L.21, S.54, D.69, L.71, T.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.69, A:T.89, A:T.89 Water bridges: A:S.54 EDO.5: 4 residues within 4Å: Chain A: E.46, Y.47, P.49 Ligands: GDP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.47 EDO.6: 6 residues within 4Å: Chain A: Q.37, L.38, N.41, R.164, V.167, D.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.164, A:D.168

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

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2B of GTPase KRas