SMTL ID : 7rt2.1

Crystal Structure of KRAS G12D with compound 25 (4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol) bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 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 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:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:K.17, A:S.18, A:S.18, A:S.18, A:Y.33, A:Y.33, A:K.148 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.2

1 x 7NL: 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol(Non-covalent)

7NL.3: 20 residues within 4Å: Chain A: G.11, D.13, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: EDO.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:E.63, A:Y.65, A:Y.65, A:R.69, A:M.73, A:Q.100, A:I.101 Hydrogen bonds: A:D.13, A:G.61, A:S.66, A:R.69, A:D.70, A:D.70, A:Y.97, A:R.103 Water bridges: A:D.13, A:E.63 Salt bridges: A:E.63

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: F.91, E.92, D.93, I.94, H.95, L.134, Y.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.91, A:I.94, A:H.95 Water bridges: A:Y.138

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

EDO.5: 7 residues within 4Å: Chain A: E.38, T.59, A.60, R.69, Y.72, M.73 Ligands: 7NL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.59, A:Y.72 Water bridges: A:Y.72

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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