SMTL ID : 9n7r.1

Crystal structure of HPK1 bound to N-(3,5-difluoro-4-{[3-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridin-4-yl]oxy}phenyl)-N'-[3-(morpholin-4-yl)propyl]urea (compound C6)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: D.68, D.69, L.181, A.182, L.185 Chain B: H.234, P.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68 EDO.2: 6 residues within 4Å: Chain A: I.149, H.150, R.151, D.170, K.204 Ligands: 01.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:D.170, A:D.170, A:K.204 EDO.3: 6 residues within 4Å: Chain A: L.38, C.109, G.110, G.112, D.116 Ligands: 01.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.109 EDO.4: 8 residues within 4Å: Chain A: Y.32, D.51, S.54, D.56, V.58, H.93, C.105 Ligands: DMS.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:D.51, A:D.56 EDO.5: 5 residues within 4Å: Chain A: P.229, L.230, P.250, R.251 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.230 EDO.6: 2 residues within 4Å: Chain A: K.253 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.253 EDO.7: 6 residues within 4Å: Chain A: F.231, D.232, V.233, H.234, P.235 Chain B: Y.192 No protein-ligand interaction detected (PLIP) EDO.15: 8 residues within 4Å: Chain A: W.193 Chain B: Q.115, Y.118, Q.119, E.222, L.226, Q.227, P.228 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.119, B:L.226 EDO.16: 7 residues within 4Å: Chain B: L.38, F.108, C.109, G.110, A.111, G.112 Ligands: 01.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.110

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: Q.115, Y.118, Q.119, E.222, L.226, Q.227, P.228, F.231 Chain B: W.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.118, A:Q.119, A:L.226 Water bridges: A:L.226

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

DMS.9: 6 residues within 4Å: Chain A: H.31, Y.32, D.51, V.53, Y.96 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.51 DMS.10: 7 residues within 4Å: Chain A: Y.43, V.46, K.61, A.156, D.170, F.171 Ligands: 01.13 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.43

5 x 01: N-(3,5-difluoro-4-{[3-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridin-4-yl]oxy}phenyl)-N'-[3-(morpholin-4-yl)propyl]urea

01.11: 21 residues within 4Å: Chain A: R.184, E.186, F.187, I.188, G.189, M.194, V.198, V.201, A.202, K.204 Chain B: Y.43, H.150, R.151, D.152, E.180, F.187, I.188, V.201, A.202, G.205, Y.207 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:I.188, A:I.188, A:V.201, B:I.188, B:I.188 Water bridges: A:K.204, B:R.151, B:E.180, B:E.180, B:Y.207 Halogen bonds: A:V.198 Hydrogen bonds: B:R.151, B:Y.207 Salt bridges: B:D.152, B:E.180 01.12: 6 residues within 4Å: Chain A: R.29, L.34, L.35, Q.36, R.37, F.47 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.34 pi-Stacking: A:F.47, A:F.47 01.13: 20 residues within 4Å: Chain A: L.38, G.39, Y.43, V.46, A.59, K.61, V.90, M.106, E.107, F.108, C.109, G.110, G.112, S.113, D.116, Q.119, L.159, A.169 Ligands: EDO.3, DMS.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.38, A:L.159 Hydrogen bonds: A:E.107, A:C.109, A:D.116, A:D.116 Water bridges: A:S.113, A:D.116 01.14: 20 residues within 4Å: Chain A: E.77, I.80, L.81, C.84, I.89, V.90, A.91, L.143, K.148, I.149, H.150, R.151, L.168, A.169, D.170, L.203, K.204, G.205 Chain B: T.243 Ligands: EDO.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.89 Hydrogen bonds: A:E.77, A:E.77, A:V.90 Water bridges: A:R.151 01.17: 18 residues within 4Å: Chain B: L.38, G.39, V.46, A.59, K.61, V.90, M.106, E.107, F.108, C.109, G.112, S.113, D.116, Q.119, L.159, A.169, F.171 Ligands: EDO.16 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.38, B:L.159 Hydrogen bonds: B:E.107, B:C.109, B:D.116, B:D.116

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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