SMTL ID : 9d0s.1

Crystal structure of human Wee1 kinase domain in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

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

NA.1: 8 residues within 4Å: Chain A: G.68, Q.69, H.70, S.71, V.73, V.74, R.75 Ligands: CL.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.73

13 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: A.99, K.142, P.143, S.144, R.195, F.196 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: R.126, R.129, V.278 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: R.195, F.196, C.223, P.229, L.230 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.18, G.20, S.21 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.244, L.245, K.261 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.92, N.94 Ligands: 01.15 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.208, P.210, K.211 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.8, E.12, F.13, K.32 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: E.200, Q.203, N.205 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.142, S.144, R.195 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: G.68, Q.69, H.70, S.71, R.75 Ligands: NA.1 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: R.43, E.82, D.83, D.84, H.85 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: S.253, Q.254, E.255 Ligand excluded by PLIP

1 x 01: (8P)-3-(2,6-dichlorophenyl)-1-methyl-8-[1-(1-methylpiperidin-4-yl)-1H-pyrazol-4-yl]-1,2,3,7-tetrahydro-4H-pyrrolo[3',2':5,6]pyrido[4,3-d]pyrimidin-4-one

01.15: 22 residues within 4Å: Chain A: E.17, I.19, G.20, V.27, A.40, I.41, K.42, H.64, V.74, I.88, N.90, E.91, Y.92, C.93, N.94, G.95, G.96, F.147, G.176, D.177, L.178 Ligands: CL.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.19, A:I.19, A:A.40, A:K.42, A:K.42, A:I.88, A:Y.92, A:F.147 Hydrogen bonds: A:N.90, A:C.93, A:C.93 Water bridges: A:S.97, A:D.100 Halogen bonds: A:A.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knight, J.L. et al., Harnessing free energy calculations for kinome-wide selectivity in drug discovery campaigns with a Wee1 case study. Nat Commun (2025)

Release Date

2025-09-10

Peptides

Wee1-like protein kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Wee1-like protein kinase

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