SMTL ID : 7dn4.1

The crystal structure of Cpd8 in complex with BPTF bromodomain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-hexamer

Ligands

6 x JC3: 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-one(Non-covalent)

JC3.1: 14 residues within 4Å: Chain A: W.36, P.37, F.38, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.42, A:A.47, A:Y.92, A:Y.92 Hydrogen bonds: A:P.37, A:N.93 Salt bridges: A:D.46 pi-Stacking: A:W.36, A:F.99 JC3.2: 15 residues within 4Å: Chain B: W.36, P.37, F.38, L.39, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.47, B:Y.92 Hydrogen bonds: B:P.37 Salt bridges: B:D.46 pi-Stacking: B:W.36 JC3.3: 15 residues within 4Å: Chain C: W.36, P.37, F.38, L.39, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.42, C:A.47, C:Y.50, C:Y.92, C:Y.92 Hydrogen bonds: C:P.37, C:N.93 Salt bridges: C:D.46 pi-Stacking: C:W.36 JC3.4: 19 residues within 4Å: Chain B: A.7, M.8, L.11, T.12 Chain D: W.36, P.37, F.38, L.39, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.47, D:Y.50, D:Y.92, D:Y.92 Hydrogen bonds: D:P.37, D:N.93 Salt bridges: D:D.46 pi-Stacking: D:W.36 JC3.5: 18 residues within 4Å: Chain A: A.7, M.8, L.11, T.12 Chain E: W.36, P.37, F.38, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:V.42, E:D.46, E:A.47, E:Y.50, E:Y.50, E:Y.92, E:Y.92 Hydrogen bonds: E:P.37, E:N.93 Salt bridges: E:D.46 pi-Stacking: E:W.36 JC3.6: 14 residues within 4Å: Chain F: W.36, P.37, F.38, E.40, P.41, V.42, D.43, D.46, A.47, Y.50, C.89, Y.92, N.93, F.99 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.42, F:A.47, F:Y.50, F:Y.92, F:Y.92 Hydrogen bonds: F:P.37, F:N.93 Salt bridges: F:D.46 pi-Stacking: F:W.36, F:F.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, L. et al., Discovery of selective BPTF bromodomain inhibitors by screening and structure-based optimization. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-10-20

Peptides

Nucleosome-remodeling factor subunit BPTF: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleosome-remodeling factor subunit BPTF

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