SMTL ID : 6s55.1

Crystal structure of human ATAD2 bromodomain in complex with N-(4-bromo-3-((3-methylpiperidin-1-yl)sulfonyl)phenyl)-2-(2,5-dioxoimidazolidin-1-yl)acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.113, A:E.114, A:E.114 EDO.2: 6 residues within 4Å: Chain A: E.10, F.14, E.114, L.115, D.116, F.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.10, A:E.10, A:E.114, A:D.116

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

SO4.3: 2 residues within 4Å: Chain A: R.29, R.99 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.99, A:R.99, A:R.99 Salt bridges: A:R.99 SO4.4: 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

1 x KW5: 2-[2,5-bis(oxidanylidene)imidazolidin-1-yl]-~{N}-[4-bromanyl-3-[(3~{S})-3-methylpiperidin-1-yl]sulfonyl-phenyl]ethanamide(Non-covalent)

KW5.5: 18 residues within 4Å: Chain A: R.29, V.30, F.31, K.33, P.34, V.35, D.36, E.39, V.40, Y.43, M.51, D.52, I.78, N.81, A.82, Y.85, N.86, I.96 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.30, A:F.31, A:V.35, A:V.40, A:D.52, A:Y.85, A:Y.85, A:I.96 Hydrogen bonds: A:R.29, A:K.33, A:K.33, A:D.36, A:N.86 Halogen bonds: A:I.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bamborough, P. et al., A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification. J.Med.Chem. (2019)

Release Date

2019-08-21

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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