SMTL ID : 9bik.1

Crystal structure of inhibitor 1 bound to HPK1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

9 x EDO: 1,2-ETHANEDIOL

EDO.1: 9 residues within 4Å: Chain A: L.81, I.89, V.90, Y.92, I.104, M.106, A.169, D.170, F.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.170 Water bridges: A:L.81, A:L.81, A:Y.92 EDO.2: 9 residues within 4Å: Chain A: C.84, R.85, H.86, A.87, I.89, V.90, A.91, R.167 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.84, A:R.167, A:R.167 EDO.3: 7 residues within 4Å: Chain A: L.81, K.82, C.84, R.85, A.91, Y.92 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.81, A:Y.92 EDO.4: 6 residues within 4Å: Chain A: Y.32, D.51, S.54, D.56, V.58, H.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:D.51 EDO.6: 10 residues within 4Å: Chain B: K.61, E.77, L.81, V.90, I.104, M.106, A.169, D.170, F.171 Ligands: 01.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.61, B:D.170 EDO.7: 9 residues within 4Å: Chain A: W.193 Chain B: Q.115, Y.118, Q.119, E.222, L.226, Q.227, P.228, F.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.119 Water bridges: B:L.226 EDO.8: 6 residues within 4Å: Chain B: R.251, L.252, H.263, N.264, I.266, K.267 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.252, B:H.263 EDO.9: 8 residues within 4Å: Chain B: G.39, G.40, S.113, Q.115, D.116, A.156, L.159 Ligands: 01.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.115 Water bridges: B:D.116, B:D.116 EDO.10: 7 residues within 4Å: Chain B: Y.32, D.51, S.54, D.56, V.58, H.93, C.105 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.32, B:D.51, B:D.51, B:D.56

2 x 01: (1S,2S)-N-[(6P)-8-amino-6-(4-methylpyridin-3-yl)isoquinolin-3-yl]-2-cyanocyclopropane-1-carboxamide

01.5: 22 residues within 4Å: Chain A: Q.36, L.38, G.39, Y.43, V.46, A.59, K.61, V.90, M.106, E.107, F.108, C.109, G.110, A.111, G.112, S.113, D.116, A.156, N.157, L.159, A.169, F.171 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.38, A:Y.43, A:L.159, A:F.171 Hydrogen bonds: A:Q.36, A:K.61, A:E.107, A:C.109, A:C.109 Water bridges: A:G.39 pi-Stacking: A:Y.43, A:Y.43 01.11: 24 residues within 4Å: Chain B: Q.36, L.38, G.41, T.42, V.46, K.48, A.59, K.61, V.90, M.106, E.107, F.108, C.109, G.110, A.111, G.112, D.116, A.156, N.157, L.159, A.169, D.170 Ligands: EDO.6, EDO.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.38, B:L.159, B:D.170 Hydrogen bonds: B:Q.36, B:K.61, B:E.107, B:C.109, B:C.109 Water bridges: B:G.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tellis, J.C. et al., Discovery of GNE-6893, a Potent, Selective, Orally Bioavailable Small Molecule Inhibitor of HPK1. Acs Med.Chem.Lett. (2024)

Release Date

2024-10-02

Peptides

Mitogen-activated protein kinase kinase kinase kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mitogen-activated protein kinase kinase kinase kinase 1

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