SMTL ID : 9nac.1

Structure of HPK1 with C4 bound at its active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.29, M.62, W.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.101 EDO.2: 2 residues within 4Å: Chain A: H.86, Q.138 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.86, A:E.135, A:Q.138, A:Q.138 EDO.3: 5 residues within 4Å: Chain A: H.144, K.147, K.148, I.149, E.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.144 EDO.8: 2 residues within 4Å: Chain B: H.144, S.145 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.144, B:T.281 EDO.9: 1 residues within 4Å: Chain B: F.231 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain B: Y.43, K.61, D.170 Ligands: 01.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:K.61, B:D.170 EDO.11: 5 residues within 4Å: Chain B: I.80, K.147, K.148, I.149, S.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.149 Water bridges: B:K.76, B:K.76 EDO.12: 2 residues within 4Å: Chain B: Q.115, A.156 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.154, B:K.154 EDO.13: 2 residues within 4Å: Chain B: H.86, Y.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.86 Water bridges: B:S.145 EDO.14: 1 residues within 4Å: Ligands: PGE.17 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: K.48, F.108, G.110 Ligands: PGE.17, 01.19 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: K.52, V.53 No protein-ligand interaction detected (PLIP) GOL.16: 4 residues within 4Å: Chain B: N.295, G.297, L.298, D.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.295, B:D.301 Water bridges: B:G.293

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

MES.5: 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.18: 6 residues within 4Å: Chain B: H.31, Y.32, D.51, V.53, S.54, Y.96 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.96 Water bridges: B:D.51, B:D.51 Salt bridges: B:D.51

2 x 01: 5-[(4-{[(1S)-2-hydroxy-1-phenylethyl]amino}-5-[3-(oxan-4-yl)-1,2,4-oxadiazol-5-yl]pyrimidin-2-yl)amino]-3,3-dimethyl-2-benzofuran-1(3H)-one

01.6: 18 residues within 4Å: Chain A: L.38, G.39, Y.43, V.46, A.59, V.90, M.106, E.107, F.108, C.109, G.110, G.112, S.113, D.116, L.159, A.169, D.170 Ligands: NA.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.38, A:L.38, A:V.46, A:V.46, A:V.90, A:M.106, A:L.159, A:A.169 Hydrogen bonds: A:E.107, A:C.109, A:D.116, A:D.170 Water bridges: A:S.113, A:F.171 01.19: 19 residues within 4Å: Chain B: L.38, G.39, Y.43, V.46, A.59, V.90, M.106, E.107, F.108, C.109, G.110, G.112, S.113, D.116, L.159, A.169, D.170 Ligands: EDO.10, EDO.15 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.38, B:V.46, B:V.46, B:V.90, B:M.106, B:L.159, B:A.169 Hydrogen bonds: B:E.107, B:C.109, B:S.113, B:D.116, B:D.170 Water bridges: B:S.113, B:D.116, B:F.171 Salt bridges: B:K.61

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

NA.7: 3 residues within 4Å: Chain A: N.157, D.170 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.170 Water bridges: A:N.157

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.17: 7 residues within 4Å: Chain B: L.35, Q.36, K.48, R.50, L.57 Ligands: EDO.14, EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.48

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: 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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