SMTL ID : 8f1g.2 (1 other biounit)

Crystal structure of human WDR5 in complex with compound WM662

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x X8N: (2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid(Non-covalent)

X8N.1: 13 residues within 4Å: Chain A: S.205, P.206, N.207, G.208, K.209, Y.210, L.222, K.232, F.248, V.250, K.254, L.270, Q.271 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.206, A:Y.210, A:Y.210, A:L.222, A:F.248, A:V.250, A:L.270 Hydrogen bonds: A:S.205, A:N.207, A:N.207, A:K.209 Salt bridges: A:K.254 pi-Stacking: A:Y.210

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: S.73, F.115, Y.242, C.243, I.287 Ligands: PGE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.73, A:C.243 GOL.3: 4 residues within 4Å: Chain A: W.41, E.62, K.63, S.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.62, A:S.99 Water bridges: A:W.41 GOL.4: 6 residues within 4Å: Chain A: I.192, D.193, W.223, G.228, K.229, C.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.230

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

SO4.5: 6 residues within 4Å: Chain A: L.125, I.137, L.146, K.147, T.182, A.183 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.147, A:K.147, A:K.147 Salt bridges: A:K.147

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 8 residues within 4Å: Chain A: A.47, G.71, I.72, S.73, D.89, Y.113, F.131 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, J. et al., Discovery of Potent Small-Molecule Inhibitors of WDR5-MYC Interaction. Acs Chem.Biol. (2023)

Release Date

2023-01-11

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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