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

Crystal structure of human WDR5 in complex with compound 9d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 5MQ: N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide(Non-covalent)

5MQ.1: 17 residues within 4Å: Chain A: A.25, 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.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.25, A:F.111, A:F.111, A:P.151, A:Y.169, A:L.299 Hydrogen bonds: A:S.69 Salt bridges: A:D.70 pi-Stacking: A:F.111

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: K.101, T.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.102 Salt bridges: A:K.101

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

EDO.3: 6 residues within 4Å: Chain A: Y.206, L.218, L.227, K.228, L.266, Q.267 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.206, A:K.228, A:K.228, A:Q.267 EDO.4: 5 residues within 4Å: Chain A: Y.238, D.280, V.281, L.299, E.300 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: T.18, G.277, T.279, D.302, T.304, K.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.277, A:K.306 EDO.6: 4 residues within 4Å: Chain A: A.20, G.21, K.48, F.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.48 EDO.7: 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.8: 4 residues within 4Å: Chain A: S.201, P.202, N.203, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.203 EDO.9: 3 residues within 4Å: Chain A: F.57, K.59, T.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.60, A:T.60, A:T.60 EDO.10: 5 residues within 4Å: Chain A: S.69, D.85, Y.109, F.111 Ligands: 5MQ.1 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: L.79, I.91, L.100, K.101, V.136, K.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.136 EDO.12: 6 residues within 4Å: Chain A: L.121, I.133, L.142, K.143, T.178, A.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.143

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

UNX.13: 1 residues within 4Å: Chain A: K.199 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: W.73, S.75, N.116 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Getlik, M. et al., Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1). J. Med. Chem. (2016)

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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