SMTL ID : 8z69.1

Crystal Structure of the second bromodomain of human BRD2 BD2 in complex with the inhibitor Y13195

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

4 x 01: 7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one

01.1: 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, D.115, V.116 Chain D: W.51 Ligands: 01.18, FMT.21 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.51, A:W.51, A:P.52, A:L.62, A:V.116 Hydrogen bonds: A:D.58, A:N.110 pi-Stacking: A:H.114, D:W.51 pi-Cation interactions: A:H.114 01.5: 17 residues within 4Å: Chain B: W.51, P.52, F.53, K.55, 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.6 12 PLIP interactions: 12 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 pi-Stacking: B:H.114 pi-Cation interactions: B:H.114 01.11: 18 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, V.116, M.119 Ligands: GOL.12, GOL.13, EDO.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.51, C:P.52, C:D.58, C:L.62, C:Y.109, C:V.116, C:V.116 Hydrogen bonds: C:D.58, C:N.110 pi-Stacking: C:H.114 pi-Cation interactions: C:H.114 01.18: 21 residues within 4Å: Chain A: W.51 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: 01.1, FMT.21, FMT.22, EDO.25 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.51, D:W.51, D:P.52, D:L.62, D:Y.109, D:V.116, D:V.116 Hydrogen bonds: D:D.58, D:N.110 pi-Stacking: D:H.114, A:W.51 pi-Cation interactions: D:H.114

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

FMT.2: 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.3: 5 residues within 4Å: Chain A: R.100, L.101, S.104 Chain B: R.100, Y.131 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.104, B:R.100, B:R.100 Water bridges: B:Y.131 FMT.4: 2 residues within 4Å: Chain A: D.115 Ligands: FMT.27 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain A: P.56, V.57, D.58 Chain C: E.85 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.57, A:A.59 FMT.16: 1 residues within 4Å: Chain C: A.97 No protein-ligand interaction detected (PLIP) FMT.19: 2 residues within 4Å: Chain D: P.112, R.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.121 FMT.20: 3 residues within 4Å: Chain D: Q.93, E.94, A.97 No protein-ligand interaction detected (PLIP) FMT.21: 4 residues within 4Å: Chain A: K.55 Chain D: K.55 Ligands: 01.1, 01.18 1 PLIP interactions: 1 interactions with chain D Water bridges: D:P.56 FMT.22: 3 residues within 4Å: Chain A: A.48 Chain D: H.114 Ligands: 01.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.114 FMT.27: 2 residues within 4Å: Chain D: D.115 Ligands: FMT.4 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain B: H.114, D.115 Ligands: 01.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.115 GOL.12: 4 residues within 4Å: Chain C: W.51, Y.54 Ligands: 01.11, GOL.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.51 Water bridges: C:Y.54 GOL.13: 3 residues within 4Å: Chain C: D.58 Ligands: 01.11, GOL.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.58 GOL.14: 4 residues within 4Å: Chain C: L.42, Y.54, K.55 Chain D: R.82 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.55, C:K.55

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

EDO.7: 4 residues within 4Å: Chain B: V.57, D.58, A.59, H.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.59, B:H.68 Water bridges: B:S.60 EDO.8: 3 residues within 4Å: Chain B: E.40, V.126, R.130 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: P.56 Chain C: S.78, K.81, R.82 Chain D: K.55 Ligands: FMT.9 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.78, C:R.82, D:K.55 Water bridges: D:K.55 EDO.15: 3 residues within 4Å: Chain C: H.114, D.115 Ligands: 01.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.115, C:D.115 Water bridges: C:H.114, C:H.114 EDO.24: 4 residues within 4Å: Chain A: K.55 Chain D: D.58, S.60, A.61 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.55 Water bridges: D:S.60 EDO.25: 4 residues within 4Å: Chain D: D.113, H.114, D.115 Ligands: 01.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.114 EDO.26: 1 residues within 4Å: Ligands: PEG.23 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 1 residues within 4Å: Chain C: R.100 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.100, C:R.100 Water bridges: C:Y.131, C:Y.131, C:Y.131 NA.28: 3 residues within 4Å: Chain D: V.57, A.59, H.68 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.59, D:S.60 Water bridges: D:H.68, D:H.68

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

PEG.23: 3 residues within 4Å: Chain D: F.129, K.133 Ligands: EDO.26 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Discovery of the First BRD4 Second Bromodomain (BD2)-Selective Inhibitors. J.Med.Chem. (2024)

Release Date

2024-12-11

Peptides

BRD2_HUMAN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BRD2_HUMAN

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