SMTL ID : 5a82.1

Crystal structure of human ATAD2 bromodomain in complex with 4-(3R,4R) -4-(3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)aminopiperidin-3- yloxymethyl)-1-thiane-1,1-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.114 Water bridges: A:D.116 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: 6 residues within 4Å: Chain A: V.30, K.33, V.35, D.36, E.39 Ligands: YEJ.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.30, A:D.36, A:E.39 Water bridges: A:R.29

1 x YEJ: 8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one(Non-covalent)

YEJ.4: 14 residues within 4Å: Chain A: R.29, V.30, V.35, E.39, V.40, Y.43, Y.85, N.86, D.90, G.92, D.93, I.96, R.99 Ligands: EDO.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:V.40, A:I.96 Hydrogen bonds: A:N.86, A:N.86, A:N.86, A:D.93

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

SO4.5: 3 residues within 4Å: Chain A: R.9, R.12, R.16 5 PLIP interactions: 5 interactions with chain A Water bridges: 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., Structure-Based Optimization of Naphthyridones Into Potent Atad2 Bromodomain Inhibitors. J.Med.Chem. (2015)

Release Date

2015-08-12

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

Related Entries With Identical Sequence