SMTL ID : 5eap.1

Crystal structure of human WDR5 in complex with compound 9e

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

5MO.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, S.153, Y.169, C.239, I.283, L.299 Ligands: GOL.2, EDO.7, UNX.17 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.111, A:F.111, A:F.111, 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: D.85, Y.109, F.111 Ligands: 5MO.1, EDO.6, EDO.7, UNX.16, UNX.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: K.199, F.241 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: A.20, G.21, K.48, F.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.48 Water bridges: A:K.48 EDO.5: 5 residues within 4Å: Chain A: W.37, E.58, K.59, V.94, S.95 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: L.66, D.85, Y.109 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.85 Water bridges: A:G.67 EDO.7: 7 residues within 4Å: Chain A: Y.169, K.237, Y.238, C.239, I.283 Ligands: 5MO.1, GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.239 EDO.8: 6 residues within 4Å: Chain A: F.244, S.245, V.246, T.247, C.287, H.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.246, A:T.247 Water bridges: A:N.243, A:F.244

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

UNX.9: 1 residues within 4Å: Chain A: K.309 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: D.302, T.304, K.306 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Chain A: H.22 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain A: P.33, N.34, S.75, D.76, S.77 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain A: N.116, Q.118, G.161, T.178 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: K.143, T.178, A.179 No protein-ligand interaction detected (PLIP) UNX.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Ligands: GOL.2 No protein-ligand interaction detected (PLIP) UNX.17: 3 residues within 4Å: Chain A: A.43 Ligands: 5MO.1, GOL.2 No protein-ligand interaction detected (PLIP) UNX.18: 1 residues within 4Å: Chain A: A.20 No protein-ligand interaction detected (PLIP) UNX.19: 3 residues within 4Å: Chain A: A.209, K.217, W.219 No protein-ligand interaction detected (PLIP) UNX.20: 2 residues within 4Å: Chain A: L.15, T.18 No protein-ligand interaction detected (PLIP) UNX.21: 3 residues within 4Å: Chain A: W.73, S.74, S.75 No protein-ligand interaction detected (PLIP) UNX.22: 2 residues within 4Å: Chain A: K.185, T.186 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
A

WD repeat-containing protein 5

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