SMTL ID : 6pgd.1

WDR5delta32 bound to peptidomimetic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x OK4: N-acetyl-L-alanyl-5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvalyl-L-valinamide(Non-covalent)

OK4.1: 21 residues within 4Å: Chain A: A.18, V.19, S.20, A.36, G.60, I.61, S.62, D.63, D.78, Y.102, F.104, C.105, F.120, S.146, A.147, F.190, Y.231, C.232, F.234, I.276, L.292 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.18, A:A.36, A:Y.102, A:F.104, A:F.120, A:I.276, A:I.276, A:L.292 Hydrogen bonds: A:S.62, A:D.78, A:C.232 pi-Stacking: 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 Water bridges: A:K.192, A:K.192, A:K.192, A:K.192, A:K.192, A:F.237, A:C.280 Salt bridges: A:K.192 SO4.3: 5 residues within 4Å: Chain A: C.219, L.220, K.221, T.222, K.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.222 Salt bridges: A:K.262 SO4.4: 1 residues within 4Å: Chain A: S.88 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.52, A:K.52

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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