SMTL ID : 5ku3.1

BRD4 bromodomain in complex with Cpd59 ((S)-1-(3-((2-fluoro-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-1-(tetrahydrofuran-3-yl)-6,7-dihydro-1H-pyrazolo[4,3-c]pyridin-5(4H)-yl)ethanone)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.24, R.27, V.28, K.31 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.27, A:R.27, A:K.31 Water bridges: A:K.31, A:T.32 EDO.2: 2 residues within 4Å: Chain A: L.30, K.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35 Water bridges: A:L.30 EDO.3: 6 residues within 4Å: Chain A: P.45, V.46, D.47, K.50, L.51 Ligands: 6XH.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.45, A:D.47 EDO.4: 5 residues within 4Å: Chain A: Q.44, P.45, G.67, T.68, K.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.44 Water bridges: A:G.67, A:K.71 EDO.5: 6 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94, I.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62 Water bridges: A:T.62 EDO.6: 2 residues within 4Å: Chain A: N.11, N.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.11, A:N.13

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

DMS.7: 4 residues within 4Å: Chain A: F.38, D.104, L.107, M.108 No protein-ligand interaction detected (PLIP) DMS.8: 1 residues within 4Å: Chain A: W.40 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.40

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: D.103, D.104, I.105 Ligands: 6XH.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.105

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

PEG.10: 5 residues within 4Å: Chain A: P.7, E.8, M.64, R.72, D.87 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.8, A:R.72, A:R.72, A:D.87 Water bridges: A:P.6, A:E.8, A:Y.77, A:D.87

1 x 6XH: 1-[3-[[2-fluoranyl-4-(1-methylpyrazol-4-yl)phenyl]amino]-1-[(3~{S})-oxolan-3-yl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]ethanone(Non-covalent)

6XH.11: 12 residues within 4Å: Chain A: W.40, P.41, F.42, V.46, L.51, L.53, Y.56, Y.98, N.99, I.105 Ligands: EDO.3, GOL.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.42, A:L.51, A:L.51, A:Y.98 Hydrogen bonds: A:N.99 Water bridges: A:P.41 pi-Stacking: A:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crawford, T.D. et al., Discovery of a Potent and Selective in Vivo Probe (GNE-272) for the Bromodomains of CBP/EP300. J. Med. Chem. (2016)

Release Date

2016-11-02

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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