SMTL ID : 9d0q.1 (1 other biounit)

Crystal structure of human Wee1 kinase domain in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x 01: 1-[(6R)-6-(2,6-dichlorophenyl)-8-methyl-2-[4-(4-methylpiperazin-1-yl)anilino]-7,8-dihydropteridin-5(6H)-yl]ethan-1-one

01.1: 21 residues within 4Å: Chain A: E.17, I.19, G.20, V.27, A.40, I.41, K.42, E.60, V.74, I.88, N.90, E.91, Y.92, C.93, N.94, G.96, D.100, F.147, G.176, D.177, L.178 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.42, A:K.42, A:V.74, A:I.88, A:Y.92, A:F.147 Hydrogen bonds: A:N.90, A:C.93, A:C.93 Salt bridges: A:D.100 Halogen bonds: A:A.40

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

NA.2: 7 residues within 4Å: Chain A: G.68, Q.69, H.70, S.71, V.73, V.74, R.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.69 Water bridges: A:R.75

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

CL.3: 6 residues within 4Å: Chain A: A.99, K.142, P.143, S.144, R.195, F.196 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.126, R.129, V.278 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: R.195, F.196, C.223, P.229, L.230 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.8, E.12, F.13, K.32 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.18, G.20, S.21 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Q.250, V.251 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: E.200, Q.203, N.205 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.46, E.82, D.83, D.84 Ligand excluded by PLIP

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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