SMTL ID : 9e5d.1

Discovery of an Orally Biovailable KRAS G12D Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 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, E.32, 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:V.30, A:E.32, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:D.13, A:Y.33, 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 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.1, H2O.2

1 x 01: methyl 3-[(7M)-1-[(1R,4R,5S)-2-azabicyclo[2.1.1]hexan-5-yl]-8-(2-cyanoethyl)-4-[3-(dimethylamino)azetidin-1-yl]-6-fluoro-7-(3-hydroxynaphthalen-1-yl)-1H-imidazo[4,5-c]quinolin-2-yl]propanoate

01.3: 18 residues within 4Å: Chain A: G.11, A.12, D.13, T.59, 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 17 PLIP interactions: 17 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:T.59, A:E.63, A:E.64, A:D.70, A:Y.97, A:Y.97, A:R.103 Water bridges: A:G.11 Salt bridges: A:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, Q. et al., Discovery of INCB159020, an Orally Bioavailable KRAS G12D Inhibitor. J.Med.Chem. (2025)

Release Date

2025-01-22

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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