SMTL ID : 8wb1.1

Crystal Structure of small molecule KN2H covalently bound to K-Ras(G12D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, D.13, G.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.2, EDO.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.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:S.18 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

EDO.3: 4 residues within 4Å: Chain A: E.32, Y.33, P.35 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.33

1 x W3T: 1-[(1~{S},5~{R})-3-[7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-2-[[(2~{R},8~{S})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]ethanone(Covalent)

W3T.4: 20 residues within 4Å: Chain A: V.10, G.11, D.13, A.60, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.13, A:Y.65, A:R.69, A:M.73, A:Y.97, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:G.61, A:R.69, A:D.70, A:D.70, A:Y.97, A:R.103 Salt bridges: A:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, L. et al., Crystal Structure of small molecule KN2H covalently bound to K-Ras(G12D). To Be Published

Release Date

2024-09-11

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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