SMTL ID : 5a83.1

Crystal structure of human ATAD2 bromodomain in complex with 4-((3R, 4R)-4-3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydroquinolin-8- yl-aminopiperidin-3-yloxymethyl)-1-thiane-1,1-dione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: V.44, I.47, K.48, P.50 Chain B: S.58 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.58, A:K.48 Hydrogen bonds: A:V.44 EDO.2: 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:L.115 EDO.3: 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.7: 5 residues within 4Å: Chain A: S.58 Chain B: V.44, I.47, K.48, P.50 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.58, B:K.48 Hydrogen bonds: B:V.44 EDO.8: 4 residues within 4Å: Chain B: E.113, E.114, L.115, D.116 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.113, B:E.114, B:L.115, B:D.116 EDO.9: 6 residues within 4Å: Chain B: E.10, F.14, E.114, L.115, D.116, F.119 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.10, B:E.10, B:E.114, B:D.116

2 x YD3: 8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methylpyridin-3-yl)-1H-quinolin-2-one(Non-covalent)

YD3.4: 13 residues within 4Å: Chain A: V.30, V.35, D.36, E.39, V.40, Y.43, Y.85, N.86, D.90, G.92, D.93, I.96, R.99 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:V.40, A:I.96 Hydrogen bonds: A:D.36, A:N.86, A:N.86, A:N.86, A:D.93 YD3.10: 13 residues within 4Å: Chain B: V.30, V.35, D.36, E.39, V.40, Y.43, Y.85, N.86, D.90, G.92, D.93, I.96, R.99 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.30, B:V.35, B:V.40, B:I.96 Hydrogen bonds: B:D.36, B:N.86, B:N.86, B:N.86, B:D.93

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

SO4.5: 4 residues within 4Å: Chain A: Q.49, K.59 Chain B: K.64 Ligands: SO4.11 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.64, A:K.59 Water bridges: A:K.59 SO4.6: 3 residues within 4Å: Chain A: R.9, R.12, R.16 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.12, A:R.12, A:R.12, A:R.16, A:H.63 Salt bridges: A:R.9, A:R.12, A:R.16 SO4.11: 4 residues within 4Å: Chain A: K.64 Chain B: Q.49, K.59 Ligands: SO4.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.64, B:K.59 Water bridges: B:K.59 SO4.12: 3 residues within 4Å: Chain B: R.9, R.12, R.16 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.12, B:R.12, B:R.12, B:R.16, B:H.63 Salt bridges: B:R.9, B:R.12, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2

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