SMTL ID : 5lj0.1

Crystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.113 Water bridges: A:D.116, A:E.117 EDO.2: 6 residues within 4Å: Chain A: E.10, F.14, E.114, L.115, D.116, F.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.10, A:E.114, A:D.116 EDO.3: 2 residues within 4Å: Chain A: R.99 Ligands: 6XX.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99, A:R.99 EDO.4: 3 residues within 4Å: Chain A: Q.121, E.124, E.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.121, A:E.124, A:E.124 Water bridges: A:E.128

1 x 6XX: 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one(Non-covalent)

6XX.5: 14 residues within 4Å: Chain A: V.30, V.35, D.36, E.39, V.40, Y.85, N.86, D.90, G.92, D.93, L.95, I.96, R.99 Ligands: EDO.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.35, A:V.40, A:L.95, A:I.96 Hydrogen bonds: A:D.36, A:Y.85, A:N.86, A:N.86, A:N.86, A:D.93

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: R.9, R.12, R.16 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.12, A:R.16, A:R.16, A:R.16, A:R.16 Salt bridges: A:R.9, A:R.12, A:R.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bamborough, P. et al., A Chemical Probe for the ATAD2 Bromodomain. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-08-31

Peptides

ATPase family AAA domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATPase family AAA domain-containing protein 2

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