SMTL ID : 5a81.1

Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R) -3-(cyclohexylmethoxy)piperidin-4-yl-amino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.114 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

1 x 78J: (3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino}-3-methyl-1,2-dihydro-1,7-naphthyridin-2-one(Non-covalent)

78J.3: 12 residues within 4Å: Chain A: V.30, V.35, V.40, Y.43, Y.85, N.86, D.90, G.92, D.93, I.96, R.99 Ligands: SO4.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:I.96 Hydrogen bonds: A:N.86, A:N.86, A:N.86, A:D.90

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

SO4.4: 3 residues within 4Å: Chain A: R.29, R.99 Ligands: 78J.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.99 Salt bridges: A:R.99 SO4.5: 3 residues within 4Å: Chain A: R.9, R.12, R.16 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.12, 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

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