SMTL ID : 7rt4.1

KRAS G12D in complex with Compound 5B (7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-4-(piperazin-1-yl)pyrido[4,3-d]pyrimidine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

GDP.1: 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.2 24 PLIP interactions: 24 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:D.31, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:D.13, A:S.18, A:S.18, A:Y.33, A:Y.33, A:Y.33 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: 3 residues within 4Å: Chain A: S.18, D.58 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.3

1 x 7IZ: 7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-4-(piperazin-1-yl)pyrido[4,3-d]pyrimidine(Non-covalent)

7IZ.3: 15 residues within 4Å: Chain A: D.13, A.60, G.61, E.63, E.64, Y.65, R.69, D.70, M.73, 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:M.73, A:Q.100, A:I.101, A:V.104, A:V.104 Hydrogen bonds: A:D.13, A:G.61, A:R.69, A:Y.97 Salt bridges: A:E.63

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: F.91, E.92, I.94, H.95, L.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.94, A:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Identification of MRTX1133, a Noncovalent, Potent, and Selective KRAS G12D Inhibitor. J.Med.Chem. (2022)

Release Date

2021-12-22

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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