SMTL ID : 7wna.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13120

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x JGR: ~{N}-[4-(4-fluoranyl-2,6-dimethyl-phenoxy)-3-[2-[4-(2-hydroxyethyloxy)-3,5-dimethyl-phenyl]-5-methyl-4-oxidanylidene-furo[3,2-c]pyridin-7-yl]phenyl]ethanesulfonamide(Non-covalent)

JGR.1: 19 residues within 4Å: Chain A: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, H.114, V.116, M.119 Chain B: A.48, W.51, M.119 Ligands: JGR.4 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.51, A:W.51, A:P.52, A:K.55, A:L.62, A:L.64, A:L.64, A:Y.109, A:V.116, A:V.116, B:A.48, B:W.51 Hydrogen bonds: A:D.58, A:N.110 pi-Stacking: A:H.114, B:W.51 pi-Cation interactions: A:H.114 JGR.4: 16 residues within 4Å: Chain A: W.51, M.119 Chain B: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, V.116 Ligands: JGR.1 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.51, B:W.51, B:P.52, B:K.55, B:L.62, B:L.64, B:V.116, A:W.51 Hydrogen bonds: B:D.58, B:N.110 pi-Stacking: B:H.114, A:W.51 JGR.6: 17 residues within 4Å: Chain C: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, H.114, V.116 Chain D: W.51, M.119 Ligands: JGR.7 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.51, C:W.51, C:P.52, C:L.62, C:L.64, C:Y.109, C:V.116, D:W.51 Hydrogen bonds: C:D.58, C:N.110 pi-Stacking: C:H.114, D:W.51, D:W.51 JGR.7: 18 residues within 4Å: Chain C: A.48, W.51, M.119 Chain D: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, D.115, V.116 Ligands: JGR.6 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.51, D:W.51, D:P.52, D:K.55, D:L.62, D:L.64, D:L.64, D:V.116, C:W.51 Hydrogen bonds: D:D.58, D:N.110 pi-Stacking: D:H.114, C:W.51 JGR.9: 20 residues within 4Å: Chain E: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, Y.109, N.110, H.114, D.115, V.116, M.119 Chain F: A.48, W.51, M.119 Ligands: JGR.10 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:W.51, E:W.51, E:P.52, E:L.62, E:L.64, E:L.64, E:Y.109, E:D.115, E:V.116, F:W.51 Hydrogen bonds: E:D.58, E:N.110 pi-Stacking: E:H.114, F:W.51 pi-Cation interactions: E:H.114 JGR.10: 17 residues within 4Å: Chain E: W.51, D.115, M.119 Chain F: W.51, P.52, F.53, K.55, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, V.116 Ligands: JGR.9 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain F pi-Stacking: E:W.51, E:W.51, F:H.114 Halogen bonds: E:D.115 Hydrophobic interactions: F:W.51, F:W.51, F:P.52, F:L.62, F:L.62, F:L.64, F:L.64, F:V.116 Hydrogen bonds: F:D.58, F:N.110 pi-Cation interactions: F:H.114

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

EDO.2: 4 residues within 4Å: Chain A: G.63, L.64, H.65, D.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.65, A:D.66 EDO.5: 5 residues within 4Å: Chain B: V.57, D.58, A.59, S.60, H.68 No protein-ligand interaction detected (PLIP)

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

PEG.3: 5 residues within 4Å: Chain A: K.55, S.78, R.82, E.85 Chain D: V.57 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.55, A:K.55, A:R.82, D:V.57 PEG.8: 4 residues within 4Å: Chain A: P.56 Chain D: S.78, R.82, E.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.82

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Isoform 4 of Bromodomain-containing protein 2

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