SMTL ID : 7ew9.1 (2 other biounits)

GDP-bound KRAS G12D in complex with TH-Z816

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.3 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 05C: 7-(8-methylnaphthalen-1-yl)-4-[(2~{R})-2-methylpiperazin-1-yl]-2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidine(Non-covalent)

05C.2: 18 residues within 4Å: Chain A: V.10, G.11, D.13, A.60, G.61, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.10, A:E.63, A:Y.65, A:M.73, A:H.96, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:D.13, A:E.63, A:Y.97 Water bridges: A:D.13 Salt bridges: A:E.63

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

GDP.3: 20 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.1 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, A:D.31, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:K.17, A:S.18, A:S.18, A:D.31, A:K.148 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

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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