SMTL ID : 7wln.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13153

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

4 x JFR: 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one(Non-covalent)

JFR.1: 16 residues within 4Å: Chain A: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, P.111, H.114, D.115, V.116 Ligands: PEG.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.51, A:W.51, A:P.52, A:D.58, A:L.62, A:Y.109, A:V.116 Hydrogen bonds: A:D.58, A:N.110, A:N.110 Water bridges: A:P.52, A:K.55 pi-Stacking: A:H.114 pi-Cation interactions: A:H.114 JFR.4: 17 residues within 4Å: Chain B: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, P.111, H.114, V.116, M.119 Ligands: GOL.5, GOL.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.51, B:P.52, B:D.58, B:L.62, B:L.62, B:Y.109, B:V.116, B:V.116 Hydrogen bonds: B:D.58, B:N.110, B:N.110 pi-Stacking: B:H.114 pi-Cation interactions: B:H.114 JFR.8: 12 residues within 4Å: Chain C: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, V.116 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.51, C:W.51, C:P.52, C:D.58, C:L.62, C:V.116 Hydrogen bonds: C:D.58, C:N.110, C:N.110 pi-Stacking: C:H.114 pi-Cation interactions: C:H.114 JFR.9: 15 residues within 4Å: Chain D: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, N.110, P.111, H.114, V.116, M.119 Ligands: PEG.12 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.51, D:P.52, D:D.58, D:L.62, D:L.62, D:V.116 Hydrogen bonds: D:D.58, D:N.110, D:N.110 pi-Stacking: D:H.114

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 2 residues within 4Å: Chain A: H.73, K.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.83

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

PEG.3: 4 residues within 4Å: Chain A: D.113, H.114, D.115 Ligands: JFR.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.113 PEG.7: 4 residues within 4Å: Chain A: P.112, R.121 Chain B: Y.49, K.122 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.49, B:K.122, A:R.121, A:R.121 PEG.12: 3 residues within 4Å: Chain D: H.114, D.115 Ligands: JFR.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.114, D:H.114, D:D.115, D:D.115

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: H.114, D.115 Ligands: JFR.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.115, B:D.115 GOL.6: 4 residues within 4Å: Chain B: D.66, I.70, Y.109 Ligands: JFR.4 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain D: W.51, Y.54, K.55 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.51 GOL.11: 3 residues within 4Å: Chain D: K.55, D.58 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.55, D:D.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structure-Based Discovery and Optimization of Furo[3,2- c ]pyridin-4(5 H )-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors. J.Med.Chem. (2022)

Release Date

2022-08-10

Peptides

Isoform 4 of Bromodomain-containing protein 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoform 4 of Bromodomain-containing protein 2

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