SMTL ID : 9nbs.1 (1 other biounit)

Structure of HPK1 with compound R2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MES.1: 6 residues within 4Å: Chain A: Y.118, Q.119, V.120, T.121, G.122, L.226 No protein-ligand interaction detected (PLIP) MES.2: 5 residues within 4Å: Chain A: L.34, L.35, Q.36, R.37, F.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.37, A:R.37

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

EDO.3: 5 residues within 4Å: Chain A: H.144, S.145, K.147, E.209, S.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.144, A:E.209 Water bridges: A:K.147, A:S.279 EDO.4: 6 residues within 4Å: Chain A: E.126, G.256, K.257, W.258, S.259 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.256, A:K.257 EDO.5: 3 residues within 4Å: Chain A: N.208, P.274, K.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.208 EDO.6: 7 residues within 4Å: Chain A: A.200, V.201, K.204, G.205, G.206, Y.207, N.208 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.204, A:G.206, A:Y.207 Water bridges: A:V.201, A:N.208 EDO.7: 7 residues within 4Å: Chain A: Y.32, D.51, S.54, D.56, V.58, H.93, C.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.32, A:D.56 EDO.8: 5 residues within 4Å: Chain A: E.126, L.127, S.259, Q.291 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.291 Water bridges: A:Q.291 EDO.9: 6 residues within 4Å: Chain A: K.275, K.276, R.277, P.278, S.279, K.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.282 EDO.10: 3 residues within 4Å: Chain A: L.35, Q.36, K.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.48 EDO.11: 6 residues within 4Å: Chain A: A.111, G.112, D.116, I.117, L.306 Ligands: 01.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.39

1 x 01: (1R,3S,5'P)-4'-chloro-3-methyl-5'-[(3M)-3-(1-methyl-2-oxo-1,2-dihydropyridin-3-yl)phenyl]-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridine]-3-carboxamide

01.12: 25 residues within 4Å: Chain A: Q.36, R.37, L.38, G.39, Y.43, V.46, A.59, K.61, E.77, L.81, V.90, M.106, E.107, F.108, C.109, G.110, A.111, G.112, S.113, D.116, L.159, A.169, D.170, F.171 Ligands: EDO.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.38, A:L.38, A:Y.43, A:Y.43, A:K.61 Hydrogen bonds: A:G.39, A:E.107, A:C.109, A:D.170 Water bridges: A:G.40, A:K.61, A:E.77, A:E.77, A:F.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walters, B.T. et al., Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions. J.Chem.Inf.Model. (2025)

Release Date

2025-06-25

Peptides

Mitogen-activated protein kinase kinase kinase kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase kinase kinase kinase 1

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