SMTL ID : 8t5i.2 (1 other biounit)

Crystal structure of human WDR5 in complex with MR4397

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ZHF: N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide(Non-covalent)

ZHF.1: 15 residues within 4Å: Chain A: S.27, S.69, F.111, F.127, P.151, S.153, Y.169, V.195, S.196, L.212, K.237, Y.238, C.239, F.241, I.283 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.111, A:Y.169, A:L.212, A:K.237, A:Y.238, A:I.283, A:I.283 Hydrogen bonds: A:C.239 pi-Stacking: A:F.111, A:Y.169

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: Y.238, D.280, E.300, N.301 Ligands: EDO.7, UNX.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.238, A:N.301 PEG.8: 9 residues within 4Å: Chain A: P.33, W.73, S.74, S.75, F.115, N.116, P.117, F.157, N.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.74, A:F.157 Water bridges: A:F.115, A:F.157

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

EDO.3: 2 residues within 4Å: Chain A: K.143, T.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.144, A:S.180 EDO.4: 4 residues within 4Å: Chain A: N.108, F.127, D.128, E.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.108, A:D.128 EDO.5: 6 residues within 4Å: Chain A: L.121, I.133, L.142, K.143, T.178, A.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.143, A:K.143 EDO.6: 4 residues within 4Å: Chain A: W.37, E.58, V.94, S.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.58 Water bridges: A:W.37, A:S.95 EDO.7: 5 residues within 4Å: Chain A: E.257, N.259, D.280, V.281 Ligands: PEG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.259, A:N.259, A:V.281

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.9: 4 residues within 4Å: Chain A: D.280, L.299, E.300 Ligands: PEG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimani, S. et al., Crystal structure of human WDR5 in complex with MR4397. To be published

Release Date

2023-08-09

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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