SMTL ID : 8gq0.1

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with STL233497

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

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

FMT.1: 2 residues within 4Å: Chain A: K.57, K.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.60 FMT.2: 4 residues within 4Å: Chain A: D.102, D.103 Ligands: FMT.3, KCL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.103 Water bridges: A:G.101, A:D.103 FMT.3: 6 residues within 4Å: Chain A: N.98, D.102, D.103, I.104 Ligands: FMT.2, KCL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98, A:I.104 FMT.4: 4 residues within 4Å: Chain A: T.18, Q.20, N.79, A.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.80 Water bridges: A:N.19, A:Q.20, A:Q.81

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

NA.5: 4 residues within 4Å: Chain A: Y.23, K.118, E.121 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.23, A:Y.23, A:E.121 NA.6: 4 residues within 4Å: Chain A: Y.95, I.96, Y.97, N.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.96

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: N.2, P.3, P.4, P.5, V.45, D.46, Y.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.3, A:D.46, A:Y.56 GOL.8: 6 residues within 4Å: Chain A: Y.23, V.27, Q.117, K.118, E.121 Ligands: NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.118, A:K.118

1 x KCL: ~{N}-[2-(1~{H}-indol-3-yl)ethyl]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine(Non-covalent)

KCL.9: 12 residues within 4Å: Chain A: W.39, P.40, V.45, L.50, L.52, Y.97, N.98, D.103, I.104, M.107 Ligands: FMT.2, FMT.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.39, A:P.40, A:V.45, A:L.50, A:L.52, A:Y.97, A:D.103, A:I.104, A:I.104 Hydrogen bonds: A:N.98 Water bridges: A:Y.55 pi-Stacking: A:Y.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.H. et al., Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study. Sci Rep (2023)

Release Date

2023-01-18

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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