SMTL ID : 6pgf.1

WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acrylamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 x OJP: N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}prop-2-enamide(Non-covalent)

OJP.1: 14 residues within 4Å: Chain A: S.20, S.62, D.63, F.104, C.105, S.146, A.147, Y.162, F.190, K.230, Y.231, C.232, F.234, I.276 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.276 Hydrogen bonds: A:S.62, A:C.232 pi-Stacking: A:F.104, A:F.234

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

SO4.2: 4 residues within 4Å: Chain A: K.192, N.236, A.279, C.280 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.236, A:C.280, A:C.280 Water bridges: A:K.192, A:K.192, A:K.192, A:K.192, A:F.237, A:T.278 Salt bridges: A:K.192 SO4.3: 2 residues within 4Å: Chain A: R.152, N.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.196 Salt bridges: A:R.152 SO4.4: 5 residues within 4Å: Chain A: C.219, L.220, K.221, T.222, K.262 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.220, A:T.222, A:T.222, A:T.222 Water bridges: A:K.262, A:K.262 Salt bridges: A:K.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dennis, M.L. et al., Fragment screening for a protein-protein interaction inhibitor to WDR5. Struct Dyn. (2019)

Release Date

2019-12-11

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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