SMTL ID : 8un3.1 (3 other biounits)

KRAS-G13D-GDP in complex with Cpd5 (1-((S)-10-(6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl)-11-chloro-7-(((2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl)methoxy)-3,4,13,13a-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-2(1H)-yl)prop-2-en-1-one)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x XOI: 1-[(5M,8aS,13R)-5-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-2-{[(2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl]methoxy}-8a,9,11,12-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-10(8H)-yl]prop-2-en-1-one(Non-covalent)

XOI.1: 24 residues within 4Å: Chain A: V.9, G.10, A.11, G.12, K.16, P.34, T.58, A.59, G.60, E.62, E.63, Y.64, R.68, D.69, M.72, K.88, D.92, H.95, Y.96, Q.99, I.100, V.103 Ligands: GDP.2, CL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.72, A:Y.96, A:V.103, A:V.103 Hydrogen bonds: A:K.16, A:E.63, A:D.69, A:Y.96 Water bridges: A:G.60 Salt bridges: A:E.62 Halogen bonds: A:Y.96

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

GDP.2: 19 residues within 4Å: Chain A: A.11, G.12, D.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: XOI.1, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.11, A:D.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:D.30, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:D.13, A:S.17, A:S.17, A:Y.32, A:Y.32, A:Y.32, A:K.147, A:K.147 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: R.102 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: Q.61, E.62, E.63, R.68 Ligands: XOI.1 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: N.26, K.42 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

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