SMTL ID : 9nbs.2 (1 other biounit)

Structure of HPK1 with compound R2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

MES.1: 9 residues within 4Å: Chain A: A.200, V.201, K.204, G.206, Y.207, N.208, P.274, K.275 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.206, A:N.208 Water bridges: A:K.275, A:K.275 Salt bridges: A:K.275

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

EDO.2: 6 residues within 4Å: Chain A: P.229, P.250, R.251, L.252, K.253, K.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.251 Water bridges: A:K.255 EDO.3: 7 residues within 4Å: Chain A: I.80, K.147, K.148, I.149, S.174, A.175, G.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.149, A:S.174, A:S.174, A:G.178 EDO.4: 9 residues within 4Å: Chain A: I.149, I.177, L.181, K.204, G.205, G.206, Y.207, N.208 Ligands: MES.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.207, A:Y.207 EDO.5: 3 residues within 4Å: Chain A: Q.248, P.249, R.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.251, A:R.251 EDO.6: 6 residues within 4Å: Chain A: A.87, N.88, Y.131, R.134, E.135, Q.138 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.134, A:E.135 Water bridges: A:A.87, A:N.88, A:E.135, A:Q.138 EDO.7: 6 residues within 4Å: Chain A: D.152, K.154, A.156, N.157, I.173 Ligands: NA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.152, A:K.154 EDO.8: 2 residues within 4Å: Chain A: Q.36, R.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.37

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

01.9: 24 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.38, A:L.38, A:Y.43, A:Y.43, A:D.170 Hydrogen bonds: A:G.39, A:E.107, A:C.109, A:D.170 Water bridges: A:G.40, A:K.61, A:K.61, A:E.77, A:D.170, A:F.171

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

NA.10: 4 residues within 4Å: Chain A: Y.43, N.157, D.170 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.157, A:N.157

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
B

Mitogen-activated protein kinase kinase kinase kinase 1

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