SMTL ID : 5vfc.1

WDR5 bound to inhibitor MM-589

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x 9BA: N-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide(Non-covalent)

9BA.1: 24 residues within 4Å: Chain A: A.24, V.25, S.26, S.41, A.42, G.66, I.67, S.68, D.69, D.84, Y.108, F.110, C.111, F.126, S.152, A.153, F.196, K.236, Y.237, C.238, I.239, F.240, I.282, L.298 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.24, A:A.42, A:Y.108, A:F.110, A:F.110, A:F.110, A:K.236, A:Y.237, A:L.298 Hydrogen bonds: A:S.68, A:S.68, A:D.84, A:F.110, A:C.238 Salt bridges: A:D.69

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

SO4.2: 3 residues within 4Å: Chain A: H.155, K.198 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.29, A:N.113, A:K.198, A:K.198, A:K.198 Salt bridges: A:H.155, A:K.198

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

EDO.3: 5 residues within 4Å: Chain A: L.120, I.132, K.142, T.177, A.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.142, A:K.142 EDO.4: 7 residues within 4Å: Chain A: W.72, S.73, S.74, F.114, N.115, P.116 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74 EDO.5: 4 residues within 4Å: Chain A: Y.205, L.217, K.227, Q.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.205, A:K.227, A:K.227, A:Q.266 EDO.6: 1 residues within 4Å: Chain A: K.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.139 EDO.7: 5 residues within 4Å: Chain A: L.78, I.90, L.99, K.100, V.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.100, A:K.100 EDO.8: 6 residues within 4Å: Chain A: K.15, F.16, A.51, Y.52, I.292, L.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.51 EDO.9: 3 residues within 4Å: Chain A: F.126, P.150, Y.168 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karatas, H. et al., Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction. J. Med. Chem. (2017)

Release Date

2017-06-28

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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