SMTL ID : 6s56.1

Crystal structure of human ATAD2 bromodomain in complex with N-(4-chloro-3-(N,N-dimethylsulfamoyl)phenyl)-2-(2,5-dioxo-3',4'-dihydro-2'H-spiro[imidazolidine-4,1'-naphthalen]-1-yl)acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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 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 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: 1 residues within 4Å: Chain A: R.99 4 PLIP interactions: 4 interactions with chain A 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 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

1 x KVZ: 2-[(4~{R})-2',5'-bis(oxidanylidene)spiro[2,3-dihydro-1~{H}-naphthalene-4,4'-imidazolidine]-1'-yl]-~{N}-[4-chloranyl-3-(dimethylsulfamoyl)phenyl]ethanamide(Non-covalent)

KVZ.5: 14 residues within 4Å: Chain A: V.30, F.31, K.33, P.34, V.35, D.36, E.39, Y.43, M.51, I.78, A.82, Y.85, N.86, I.96 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.35 Hydrogen bonds: A:K.33, A:D.36, A:E.39, 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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