SMTL ID : 7wvk.1

Crystal structure of human WDR5 in complex with compound 19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x 6IQ: 1-[2,5-bis(chloranyl)phenyl]sulfonylbenzimidazole(Non-covalent)

6IQ.1: 12 residues within 4Å: Chain A: S.202, P.203, N.204, Y.207, F.245, S.246, V.247, K.251, W.252, L.267, Q.268 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.245, A:V.247, A:K.251, A:L.267 Hydrogen bonds: A:N.204 Halogen bonds: A:W.252

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.105, G.106, R.133, C.142, T.145 Ligands: EDO.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.105, A:R.133, A:T.145, A:T.145 Water bridges: A:C.142, A:C.142, A:C.142 GOL.6: 3 residues within 4Å: Chain A: L.16, G.278, K.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.278 Water bridges: A:G.278, A:K.307 GOL.7: 9 residues within 4Å: Chain A: N.117, Q.119, N.121, L.122, F.158, D.161, G.162, T.179 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.117, A:Q.119, A:N.121, A:N.121, A:G.162 GOL.8: 3 residues within 4Å: Chain A: T.269, K.270, E.271 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.270, A:K.270 Water bridges: A:T.230, A:T.230, A:K.270, A:E.271

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

EDO.3: 3 residues within 4Å: Chain A: C.142, T.145 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.145 EDO.4: 5 residues within 4Å: Chain A: Y.239, D.281, L.300, E.301, N.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.301, A:N.302 EDO.5: 7 residues within 4Å: Chain A: Y.207, L.219, L.228, K.229, L.267, Q.268 Ligands: 6IQ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.268 EDO.9: 5 residues within 4Å: Chain A: L.122, K.144, T.179, A.180 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144, A:T.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, Q.L. et al., Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma. Acta Pharmacol.Sin. (2023)

Release Date

2022-10-19

Peptides

WD repeat-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

WD repeat-containing protein 5

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