SMTL ID : 3smr.3 (3 other biounits)

Crystal structure of human WD repeat domain 5 with compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x NP7: 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide(Non-covalent)

NP7.1: 13 residues within 4Å: Chain A: S.27, S.28, A.43, I.68, S.69, D.70, D.85, F.111, P.151, S.153, Y.169, C.239, I.283 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.43 Hydrogen bonds: A:S.69 Salt bridges: A:D.70 pi-Stacking: A:F.111

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

EDO.2: 5 residues within 4Å: Chain A: V.9, G.249, K.250, W.251, N.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.250 Water bridges: A:K.250 EDO.3: 4 residues within 4Å: Chain A: Y.238, D.280, E.300, N.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.238, A:Y.238, A:N.301 EDO.4: 5 residues within 4Å: Chain A: T.18, T.279, D.302, T.304, K.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.304, A:K.306, A:K.306 EDO.5: 6 residues within 4Å: Chain A: K.16, F.17, A.52, Y.53, I.293, L.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.52 EDO.6: 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

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

UNX.7: 2 residues within 4Å: Chain A: E.36, W.37 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain A: D.85 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain A: W.37 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: W.73, F.115, N.116 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: Q.276, G.277 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain A: G.21, K.48, F.57 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senisterra, G. et al., Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5. Biochem. J. (2013)

Release Date

2011-08-31

Peptides

WD repeat-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

WD repeat-containing protein 5

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