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SMTL ID : 5vbo.1

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH LRRK2-IN-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x 4K4: 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one(Non-covalent)

4K4.1:

14 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
Ligands: EDO.6, EDO.8

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:W.40, A:L.53, A:Y.98, A:Y.98
Hydrogen bonds: A:N.99
Water bridges: A:Q.44, A:Q.44, A:P.45, A:D.47

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2:	2 residues within 4Å: Chain A: K.58, K.61 Ligand excluded by PLIP
CL.3:	5 residues within 4Å: Chain A: N.3, P.4, P.5, P.6, P.45 Ligand excluded by PLIP

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

EDO.4:	8 residues within 4Å: Chain A: R.17, T.19, Q.21, L.22, W.79, N.80, A.81, Q.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.19, A:A.81 Water bridges: A:N.20
EDO.5:	7 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, 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
EDO.6:	7 residues within 4Å: Chain A: Q.37, F.38, A.39, W.40, P.41, M.108 Ligands: 4K4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.37, A:W.40 Water bridges: A:Q.37, A:A.39
EDO.7:	4 residues within 4Å: Chain A: Q.18, Q.23, L.26, R.27 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.18, A:Q.23, A:R.27, A:R.27
EDO.8:	5 residues within 4Å: Chain A: N.99, D.103, D.104, I.105 Ligands: 4K4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.99, A:D.104, A:I.105

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

2018-04-04

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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