SMTL ID : 5eal.2 (1 other biounit)

Crystal structure of human WDR5 in complex with compound 9h

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 5ML: 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide(Non-covalent)

5ML.1: 17 residues within 4Å: Chain A: S.27, S.28, A.43, G.67, I.68, S.69, D.70, F.111, F.127, P.151, S.153, Y.169, C.239, I.283, L.299 Ligands: EDO.4, EDO.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.111, A:F.111, A:F.111, A:P.151, A:Y.169, A:I.283, A:L.299 Hydrogen bonds: A:S.69 Salt bridges: A:D.70 pi-Stacking: A:F.111, A:F.127, A:Y.169

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

EDO.2: 4 residues within 4Å: Chain A: Y.206, L.218, K.228, Q.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.206, A:Q.267 Water bridges: A:K.228, A:Q.267 EDO.3: 6 residues within 4Å: Chain A: L.121, I.133, L.142, K.143, T.178, A.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.143, A:K.143 EDO.4: 6 residues within 4Å: Chain A: Y.169, K.237, Y.238, C.239 Ligands: 5ML.1, EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.239 EDO.5: 5 residues within 4Å: Chain A: W.37, I.49, E.58, K.59, V.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.58, A:E.58, A:K.59 EDO.6: 4 residues within 4Å: Chain A: D.85, F.111 Ligands: 5ML.1, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85 EDO.7: 4 residues within 4Å: Chain A: L.100, K.101, V.136, K.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.101 EDO.8: 5 residues within 4Å: Chain A: T.18, T.279, D.302, T.304, K.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.279, A:T.304, A:K.306, A:K.306 EDO.9: 5 residues within 4Å: Chain A: P.33, W.73, S.75, F.115, N.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.115 Water bridges: A:W.73, A:W.73 EDO.10: 5 residues within 4Å: Chain A: Y.238, D.280, L.299, E.300, N.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.300, A:N.301

11 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.11: 3 residues within 4Å: Chain A: D.76, N.78, L.79 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: C.99, T.102 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain A: N.116, L.121, G.161, T.178 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: P.146, R.174, W.176 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain A: G.21, K.48, F.57 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: A.209, K.217, W.219 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain A: P.146, H.148 No protein-ligand interaction detected (PLIP) UNX.18: 3 residues within 4Å: Chain A: N.12, K.16, K.309 No protein-ligand interaction detected (PLIP) UNX.19: 1 residues within 4Å: Chain A: K.269 No protein-ligand interaction detected (PLIP) UNX.20: 3 residues within 4Å: Chain A: I.61, S.62, G.97 No protein-ligand interaction detected (PLIP) UNX.21: 2 residues within 4Å: Chain A: D.213, N.214 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DOMBROVSKI, L. et al., Crystal structure of human WDR5 in complex with compound 9h. to be published

Release Date

2015-11-04

Peptides

WD repeat-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

WD repeat-containing protein 5

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