SMTL ID : 9bj1.1

Crystal structure of inhibitor GNE-6893 bound to HPK1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 8 residues within 4Å: Chain A: A.200, V.201, K.204, G.206, Y.207, N.208, P.274, K.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.206, A:N.208 MES.9: 8 residues within 4Å: Chain B: A.200, V.201, K.204, G.206, Y.207, N.208, P.274, K.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.206, B:N.208 Water bridges: B:N.208 MES.10: 6 residues within 4Å: Chain B: I.23, F.24, N.25, R.26, H.31, Y.96 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.23, B:N.25, B:R.26 Salt bridges: B:R.26

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

EDO.2: 10 residues within 4Å: Chain A: T.190, P.191, Y.192, W.193, M.194 Chain B: R.151, D.152, I.153, K.154, S.215 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.191, A:W.193, B:D.152, B:I.153 EDO.3: 7 residues within 4Å: Chain A: K.61, D.152, D.170, G.172, I.173, Q.176 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.170 Water bridges: A:G.172 EDO.4: 7 residues within 4Å: Chain A: G.39, T.42, Y.43, Q.115, D.116, Q.119 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.42, A:Y.43, A:Y.43, A:Q.115 EDO.12: 6 residues within 4Å: Chain B: Y.32, D.51, S.54, D.56, V.58, H.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.32, B:D.51, B:D.51, B:H.93 EDO.13: 6 residues within 4Å: Chain B: A.87, N.88, E.135, E.165, V.166, R.167 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.135, B:R.167, B:R.167 Water bridges: B:N.88, B:E.165

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 9 residues within 4Å: Chain A: K.61, E.77, L.81, V.90, M.106, A.169, D.170, F.171 Ligands: 01.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.77, A:D.170, A:F.171 Salt bridges: A:E.77 DMS.6: 7 residues within 4Å: Chain A: T.42, Y.43, G.44, K.61, D.170 Ligands: EDO.3, 01.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61 Salt bridges: A:D.170 DMS.14: 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:Y.118 pi-Cation interactions: B:F.231

1 x 01: (9S)-2-{[(6P)-8-amino-6-(5-amino-4-methylpyridin-3-yl)-7-fluoroisoquinolin-3-yl]amino}-6-methyl-5,6-dihydro-4H-pyrazolo[1,5-d][1,4]diazepin-7(8H)-one

01.7: 25 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, D.170 Ligands: EDO.4, DMS.5, DMS.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.38, A:Y.43, A:Y.43, A:A.59, A:L.159, A:L.159 Hydrogen bonds: A:G.39, A:K.61, A:E.107, A:C.109, A:C.109, A:N.157, A:D.170

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 9 residues within 4Å: Chain A: R.37, L.38, G.39, G.40, G.41, T.42, Y.43, G.44, V.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.41, A:Y.43

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 5 residues within 4Å: Chain B: G.293, N.295, G.297, L.298, D.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.295

1 x 02: (4S,5R,7R,11aP)-10-{[(3R)-3-hydroxy-1-methyl-2-oxopyrrolidin-3-yl]ethynyl}-N~3~-methyl-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide

02.15: 27 residues within 4Å: Chain B: L.38, G.39, G.40, G.41, T.42, V.46, A.59, K.61, E.77, L.81, I.89, V.90, A.91, Y.92, I.104, M.106, E.107, F.108, C.109, G.110, A.111, G.112, L.159, A.169, D.170, F.171, G.172 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.46, B:L.81, B:I.104, B:D.170 Hydrogen bonds: B:E.77, B:E.107, B:C.109, B:C.109, B:D.170, B:F.171

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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