SMTL ID : 8f1g.1 (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: 12 residues within 4Å: Chain A: S.205, P.206, N.207, G.208, K.209, Y.210, L.222, K.232, V.250, K.254, L.270, Q.271 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.210, A:Y.210, A:L.222, A:K.254, A:L.270, A:L.270 Hydrogen bonds: A:S.205, A:N.207, A:N.207, A:K.209 pi-Stacking: A:Y.210

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.115, Y.242, C.243, I.287 Ligands: PGE.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.243 GOL.3: 4 residues within 4Å: Chain A: W.41, E.62, K.63, S.99 No protein-ligand interaction detected (PLIP) GOL.4: 7 residues within 4Å: Chain A: I.192, D.193, D.194, W.223, G.228, K.229, C.230 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.192, A:D.193, A:D.194, A:D.194, A:C.230, A:C.230 GOL.5: 5 residues within 4Å: Chain A: K.14, P.15, N.296, S.314, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.296, A:S.314

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

SO4.6: 6 residues within 4Å: Chain A: L.125, I.137, L.146, K.147, T.182, A.183 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.147 Salt bridges: A:K.147

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

PGE.7: 5 residues within 4Å: Chain A: G.71, I.72, S.73, D.89 Ligands: GOL.2 No protein-ligand interaction detected (PLIP)

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
A

WD repeat-containing protein 5

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