SMTL ID : 5i88.1

BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 7 residues within 4Å: Chain A: S.10, N.11, P.12, K.14, K.16, N.75, Y.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.11 Water bridges: A:N.11, A:Y.77

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

EDO.2: 2 residues within 4Å: Chain A: W.40, Q.44 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.61, A:T.62, A:T.62, A:N.94

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

DMS.4: 4 residues within 4Å: Chain A: Q.44, P.45, T.68, K.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.68 Salt bridges: A:D.65

1 x 69G: 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide(Non-covalent)

69G.5: 13 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, M.64, D.65, C.95, Y.98, N.99, I.105 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.40, A:P.41, A:F.42, A:V.46, A:L.51, A:L.51, A:L.53, A:D.65, A:I.105 Hydrogen bonds: A:N.99, A:N.99

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.1, T.2, P.54, Y.57, K.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.2, A:Y.57 Water bridges: A:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crawford, T.D. et al., Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J.Med.Chem. (2016)

Release Date

2016-10-12

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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