SMTL ID : 6czu.1

BRD4(BD1) complexed with 3219

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x FP7: 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-({4-[(1R)-1-hydroxyethyl]phenyl}methyl)pyridin-2(1H)-one(Covalent)

FP7.1: 9 residues within 4Å: Chain A: W.40, P.41, F.42, L.51, L.53, N.99, D.104, I.105, M.108 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:P.41, A:P.41, A:F.42, A:L.51, A:L.53, A:M.108 Hydrogen bonds: A:N.99

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

EDO.2: 1 residues within 4Å: Chain A: N.13 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.13, A:N.13, A:N.13 EDO.3: 7 residues within 4Å: Chain A: S.10, N.11, K.14, K.16, N.75, Y.77 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.11 Water bridges: A:P.12 EDO.4: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:N.94 EDO.6: 4 residues within 4Å: Chain A: Q.21, A.81, Q.82, I.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.21, A:Q.82, A:E.127 Water bridges: A:A.81 EDO.7: 3 residues within 4Å: Chain A: T.32, K.35, H.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.32 EDO.8: 4 residues within 4Å: Chain A: K.16, R.17, Q.18 Ligands: DMS.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.18 EDO.9: 7 residues within 4Å: Chain A: P.12, N.13, K.14, P.15, K.16 Ligands: EDO.3, DMS.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.12, A:N.13

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

DMS.5: 2 residues within 4Å: Ligands: EDO.8, EDO.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kharenko, O.A. et al., Design and Characterization of Novel Covalent Bromodomain and Extra-Terminal Domain (BET) Inhibitors Targeting a Methionine. J. Med. Chem. (2018)

Release Date

2018-09-26

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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