SMTL ID : 7wmq.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13157

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

4 x JFL: 2-(2-cyclobutyl-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)

JFL.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, V.116, M.119 Ligands: FMT.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:P.52, A:D.58, A:L.62, A:Y.109, A:V.116, A:V.116 Hydrogen bonds: A:D.58, A:N.110, A:N.110 pi-Stacking: A:H.114, A:H.114 JFL.8: 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, D.115, V.116, M.119 Ligands: FMT.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.51, B:W.51, B:P.52, B:L.62, B:Y.109, B:V.116 Hydrogen bonds: B:N.110, B:N.110 pi-Stacking: B:H.114, B:H.114 JFL.15: 17 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, P.111, H.114, D.115, V.116, M.119 Ligands: FMT.17 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.51, C:W.51, C:P.52, C:D.58, C:L.62, C:L.62, C:L.62, C:Y.109, 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 JFL.21: 17 residues within 4Å: Chain D: 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, M.119 Ligands: GOL.23 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: 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, D:H.114

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: L.42, Y.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.42 GOL.9: 5 residues within 4Å: Chain B: P.56, V.57, H.68, P.74 Ligands: FMT.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.57 Water bridges: B:Y.67 GOL.10: 5 residues within 4Å: Chain B: D.66, I.70, Y.109 Ligands: FMT.7, FMT.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.109 GOL.16: 4 residues within 4Å: Chain A: R.82 Chain C: K.55, S.78, R.82 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.78, C:S.78, C:R.82, A:R.82 GOL.22: 3 residues within 4Å: Chain D: K.55, D.58, A.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.55, D:K.55 GOL.23: 3 residues within 4Å: Chain D: H.114, D.115 Ligands: JFL.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.115, D:D.115

15 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 4 residues within 4Å: Chain A: G.36, I.37, E.40, R.130 No protein-ligand interaction detected (PLIP) FMT.4: 3 residues within 4Å: Chain A: S.78, K.81, R.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.82 FMT.5: 1 residues within 4Å: Chain A: D.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 FMT.6: 3 residues within 4Å: Chain A: H.114, D.115 Ligands: JFL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.115 Water bridges: A:H.114 FMT.7: 5 residues within 4Å: Chain A: K.133 Chain B: Y.109, N.110, P.111 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) FMT.11: 3 residues within 4Å: Chain B: H.114, D.115 Ligands: JFL.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.115 FMT.12: 2 residues within 4Å: Chain B: P.74 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) FMT.13: 4 residues within 4Å: Chain A: Y.109, N.110, P.111 Chain B: K.133 No protein-ligand interaction detected (PLIP) FMT.14: 3 residues within 4Å: Chain A: K.133 Chain B: K.108 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.133 FMT.17: 3 residues within 4Å: Chain C: H.114, D.115 Ligands: JFL.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.115 FMT.18: 4 residues within 4Å: Chain C: L.42, Y.54, K.55, S.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.54, C:K.55 FMT.19: 4 residues within 4Å: Chain C: K.133 Chain D: Y.109, N.110, P.111 No protein-ligand interaction detected (PLIP) FMT.20: 4 residues within 4Å: Chain C: D.66, I.70, Y.109 Ligands: FMT.24 No protein-ligand interaction detected (PLIP) FMT.24: 4 residues within 4Å: Chain C: Y.109, P.111 Chain D: K.133 Ligands: FMT.20 No protein-ligand interaction detected (PLIP) FMT.25: 2 residues within 4Å: Chain D: D.66, Y.109 No protein-ligand interaction detected (PLIP)

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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