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SMTL ID : 5v67.1

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH Volasertib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x IBI: N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide(Non-covalent)

IBI.1:

12 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, Y.56, C.95, Y.98, N.99, I.105

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:V.46, A:Y.56, A:Y.98
Hydrogen bonds: A:N.99
Water bridges: A:Q.44
pi-Stacking: A:W.40

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

EDO.2:

8 residues within 4Å:

Chain A: I.59, I.60, K.61, T.62, P.63, T.90, 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, A:N.94

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

DMS.3:	2 residues within 4Å: Chain A: K.58, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61 Water bridges: A:K.58
DMS.4:	1 residues within 4Å: Chain A: I.97 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Karim, R.M. et al., Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J.Med.Chem. (2021)

Release Date

2018-03-28

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Bromodomain-containing protein 4

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2oss.1 | 2yel.1 | 3mxf.1 | 3p5o.1 | 3svf.1 | 3svg.1 | 3u5j.1 | 3u5k.1 | 3u5k.2 | 3u5k.3 | 3u5k.4 | 3u5l.1 | 3uvw.1 | 3uvx.1 | 3uvy.1 | 3uw9.1 | 3uw9.2 | 3zyu.1 | 3zyu.2 | 4a9l.1 | 4bw1.1 | 4bw2.1 | 4bw3.1 | 4bw4.1 | 4c67.1 | 4cfk.1 | 4cfl.1 | 4cl9.1 | 4clb.1 | 4e96.1 more...less...

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