SMTL ID : 7ewa.1 (2 other biounits)

GDP-bound KRAS G12D in complex with TH-Z827

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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.2, H2O.2

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

GDP.2: 19 residues within 4Å: Chain A: 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.1 26 PLIP interactions: 26 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, A:K.148, A:K.148 Water bridges: A:D.13, A:K.17, A:K.17, A:S.18, A:S.18, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

1 x 05F: 4-[(1~{R},5~{S})-3,8-diazabicyclo[3.2.1]octan-8-yl]-7-(8-methylnaphthalen-1-yl)-2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidine(Non-covalent)

05F.3: 18 residues within 4Å: Chain A: G.11, A.12, D.13, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.63, A:Y.65, A:R.69, A:M.73, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:D.13, A:Y.65, A:Y.97 Water bridges: A:G.61 Salt bridges: A:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mao, Z. et al., KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge. Cell Discov (2022)

Release Date

2021-12-29

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2B of GTPase KRas

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