SMTL ID : 4ia9.1

Crystal structure of human WD REPEAT DOMAIN 5 in complex with 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x IA9: 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide(Non-covalent)

IA9.1: 18 residues within 4Å: Chain A: A.25, S.27, S.28, S.42, A.43, G.67, I.68, S.69, D.70, D.85, F.111, P.151, S.153, Y.169, C.239, I.283, L.299 Ligands: UNX.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.25, A:A.43 Hydrogen bonds: A:S.69 Salt bridges: A:D.70 pi-Stacking: A:F.111

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

EDO.2: 4 residues within 4Å: Chain A: W.37, E.58, K.59, S.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.58 EDO.3: 4 residues within 4Å: Chain A: Y.238, D.280, L.299, E.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.300 Water bridges: A:D.280, A:V.281

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

UNX.4: 4 residues within 4Å: Chain A: L.15, F.17, T.18 Ligands: UNX.25 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: Y.53 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: L.46, S.62 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: K.98, C.99 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Chain A: K.199 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: Q.118, N.120 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: N.108, Y.109 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: T.229, K.269 Ligand excluded by PLIP UNX.12: 2 residues within 4Å: Chain A: K.237, Y.238 Ligand excluded by PLIP UNX.13: 1 residues within 4Å: Chain A: I.271 Ligand excluded by PLIP UNX.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.15: 1 residues within 4Å: Chain A: E.36 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: P.151 Ligands: IA9.1 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: A.20, G.21 Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain A: N.116, G.161, T.178 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: T.18, L.19, G.55 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: G.277, T.279 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: N.214, H.233 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: L.66, G.67 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain A: D.86, T.88 Ligand excluded by PLIP UNX.24: 1 residues within 4Å: Chain A: Q.267 Ligand excluded by PLIP UNX.25: 1 residues within 4Å: Ligands: UNX.4 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain A: W.73, S.75 Ligand excluded by PLIP UNX.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolshan, Y. et al., Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction. ACS Med Chem Lett (2013)

Release Date

2012-12-26

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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