SMTL ID : 6yb4.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

SO4.1: 1 residues within 4Å: Chain A: R.99 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.29, A:R.29, A:R.99 Salt bridges: A:R.99 SO4.2: 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

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

EDO.3: 4 residues within 4Å: Chain A: V.44, I.47, K.48, P.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.47 EDO.4: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 No protein-ligand interaction detected (PLIP) EDO.5: 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

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

OJH.6: 17 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, I.78, N.81, A.82, Y.85, N.86, I.96 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.35, A:V.40 Hydrogen bonds: A:R.29, A:K.33, A:D.36, A:E.39, A:N.86 pi-Stacking: A:F.31 Halogen bonds: A:I.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucas, S.C.C. et al., Optimization of Potent ATAD2 and CECR2 Bromodomain Inhibitors with an Atypical Binding Mode. J.Med.Chem. (2020)

Release Date

2020-05-06

Peptides

ATPase family AAA domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

ATPase family AAA domain-containing protein 2

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