SMTL ID : 5mq1.1

Crystal structure of the BRD7 bromodomain in complex with BI-9564

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 5U6: 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one(Non-covalent)

5U6.1: 12 residues within 4Å: Chain A: S.26, A.27, F.28, F.29, F.31, P.32, V.33, I.37, A.38, N.84, Y.90 Ligands: CL.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.37, A:I.37, A:I.37, A:Y.90 Hydrogen bonds: A:N.84 Water bridges: A:T.34 pi-Stacking: A:Y.90, A:Y.90

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: E.67, K.70, D.71 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.67, A:D.71, A:D.71 ZN.3: 3 residues within 4Å: Chain A: H.99 Ligands: CL.4, CL.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.99

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

CL.4: 6 residues within 4Å: Chain A: M.81, K.95, L.98, H.99 Ligands: ZN.3, CL.5 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: K.95, H.99 Ligands: ZN.3, CL.4 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Ligands: 5U6.1 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.8: 5 residues within 4Å: Chain A: K.23, D.24, P.25, S.26, A.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.26, A:S.26 Water bridges: A:K.23, A:K.96 EDO.9: 2 residues within 4Å: Chain A: T.34, D.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.35 EDO.10: 2 residues within 4Å: Chain A: F.36, I.37 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: I.44, I.82, Y.83, K.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.85 Water bridges: A:K.85, A:K.85, A:K.85 EDO.12: 4 residues within 4Å: Chain A: K.74, L.98, H.99, M.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.74, A:K.74 Water bridges: A:H.99, A:H.99 EDO.13: 4 residues within 4Å: Chain A: K.95, K.96, H.99 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.96 EDO.14: 2 residues within 4Å: Chain A: K.23, I.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.23 EDO.15: 4 residues within 4Å: Chain A: I.44, I.45, K.46, H.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.46, A:H.47 EDO.16: 3 residues within 4Å: Chain A: K.92, K.96 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.92 EDO.17: 1 residues within 4Å: Chain A: I.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.110 EDO.18: 3 residues within 4Å: Chain A: K.23, S.100, K.103 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.23, A:S.100, A:S.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Crystal structure of the BRD7 bromodomain in complex with BI-9564. To Be Published

Release Date

2018-01-17

Peptides

Bromodomain-containing protein 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 7