SMTL ID : 8un4.1

KRAS-G13D-GDP in complex with Cpd36 ((E)-1-((3S)-4-(7-(6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl)-6-chloro-8-fluoro-2-(((S)-2-methylenetetrahydro-1H-pyrrolizin-7a(5H)-yl)methoxy)quinazolin-4-yl)-3-methylpiperazin-1-yl)-3-(4-((dimethylamino)methyl)-5-methylpyridin-2-yl)prop-2-en-1-one)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.3

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

GDP.2: 21 residues within 4Å: Chain A: A.12, G.13, D.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1, XV3.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:D.31 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x XV3: (2E)-1-{(3S)-4-[(7M)-7-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-8-fluoro-2-{[(4R,7aS)-2-methylidenetetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}quinazolin-4-yl]-3-methylpiperazin-1-yl}-3-{4-[(dimethylamino)methyl]-5-methylpyridin-2-yl}prop-2-en-1-one(Non-covalent)

XV3.3: 27 residues within 4Å: Chain A: V.10, G.11, A.12, G.13, D.14, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, F.79, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.35, A:E.63, A:M.73, A:H.96, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:K.17, A:Y.65, A:D.70, A:D.70, A:Y.97 Water bridges: A:E.64, A:E.64, A:E.64 Salt bridges: A:D.14, A:E.63 Halogen bonds: A:Y.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nilewski, C. et al., Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors. Acs Med.Chem.Lett. (2024)

Release Date

2023-12-20

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas