SMTL ID : 8ujy.1

Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x VV3: (9P)-4-[(3,5-dimethoxyphenyl)methyl]-9-(4-fluoro-2-methylphenyl)-7-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-3,4-dihydro-1,4-benzoxazepin-5(2H)-one(Non-covalent)

VV3.1: 26 residues within 4Å: Chain A: A.25, V.26, S.27, S.28, A.43, G.67, I.68, S.69, D.70, D.85, F.111, C.112, F.127, P.151, V.152, S.153, A.154, Y.169, F.197, K.237, Y.238, C.239, I.240, F.241, I.283, L.299 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.25, A:A.43, A:P.151, A:I.283, A:I.283, A:L.299 Hydrogen bonds: A:C.239, A:C.239 Salt bridges: A:D.70 pi-Stacking: A:F.111, A:F.111, A:Y.169, A:F.241 VV3.2: 26 residues within 4Å: Chain B: A.25, V.26, S.27, S.28, A.43, G.67, I.68, S.69, D.70, D.85, F.111, C.112, F.127, P.151, V.152, S.153, A.154, Y.169, F.197, K.237, Y.238, C.239, I.240, F.241, I.283, L.299 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.25, B:A.43, B:F.127, B:I.283, B:I.283, B:L.299 Hydrogen bonds: B:C.239, B:C.239 Water bridges: B:S.69 pi-Stacking: B:F.111, B:Y.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teuscher, K.B. et al., Structure-Based Discovery of Potent, Orally Bioavailable Benzoxazepinone-Based WD Repeat Domain 5 Inhibitors. J.Med.Chem. (2023)

Release Date

2023-12-20

Peptides

WD repeat-containing protein 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

WD repeat-containing protein 5

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