5khm.1 | SWISS-MODEL Template Library

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SMTL ID : 5khm.1

The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

1 x XNH: (3~{R})-4-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)piperidin-4-yl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one(Non-covalent)

XNH.1:

20 residues within 4Å:

Chain A: P.41, F.42, V.46, L.53, Y.56, C.95, Y.98, N.99, D.104, I.105, M.108
Chain B: W.40, P.41, F.42, V.46, Y.98, N.99, D.104, I.105
Ligands: GOL.2

12 PLIP interactions:

8 interactions with chain A, 4 interactions with chain B

Hydrophobic interactions: A:P.41, A:L.53, A:Y.56, A:Y.98, A:D.104, A:I.105, A:I.105, B:W.40, B:D.104, B:I.105
Hydrogen bonds: A:N.99, B:N.99

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	6 residues within 4Å: Chain A: F.38, D.104, L.107, M.108 Chain B: L.51 Ligands: XNH.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:N.52, B:N.52 Hydrogen bonds: A:D.104
GOL.3:	6 residues within 4Å: Chain B: I.59, I.60, K.61, T.62, N.94, I.97 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.61, B:T.62, B:N.94, B:N.94
GOL.4:	2 residues within 4Å: Chain B: S.10, N.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.10 Water bridges: B:N.75

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bradbury, R.H. et al., Optimization of a Series of Bivalent Triazolopyridazine Based Bromodomain and Extraterminal Inhibitors: The Discovery of (3R)-4-[2-[4-[1-(3-Methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153). J.Med.Chem. (2016)

Release Date

2016-09-21

Peptides

Bromodomain-containing protein 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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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