SMTL ID : 4qqe.1

Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 37F: N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide(Non-covalent)

37F.1: 18 residues within 4Å: Chain A: A.25, S.27, S.28, A.43, G.67, I.68, S.69, D.70, D.85, F.111, F.127, P.151, S.153, Y.169, C.239, I.283, L.299 Ligands: UNX.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.43, A:F.111, A:F.111, A:F.111, A:F.127, A:P.151, A:Y.169, A:Y.169, A:Y.169 Hydrogen bonds: A:S.69, A:D.85 Salt bridges: A:D.70 pi-Stacking: A:F.111

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.59, T.60 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: Y.238, D.280, L.299, E.300, N.301 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.300 EDO.4: 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.5: 8 residues within 4Å: Chain A: P.33, W.73, S.74, S.75, F.115, N.116, P.117, S.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.73 Water bridges: A:W.73

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

UNX.6: 3 residues within 4Å: Chain A: D.85, F.111 Ligands: 37F.1 No protein-ligand interaction detected (PLIP) UNX.7: 3 residues within 4Å: Chain A: H.156, K.199 Ligands: UNX.8 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: K.199, F.241 Ligands: UNX.7 No protein-ligand interaction detected (PLIP) UNX.9: 6 residues within 4Å: Chain A: S.69, A.83, S.84, D.85, V.110, F.111 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: S.201, Y.206 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: K.143, T.178, A.179 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: T.229, K.269 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dombrovski, L. et al., Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345. To be Published

Release Date

2014-07-30

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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