SMTL ID : 5a5r.1

Crystal structure of human ATAD2 bromodomain in complex with 5-5- methoxypyridin-3-yl-3-methyl-8-piperidin-4-ylamino-1,2-dihydro-1,7- naphthyridin-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.10, 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.2: 3 residues within 4Å: Chain A: E.113, E.114, D.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.115 Water bridges: A:E.114 EDO.7: 5 residues within 4Å: Chain B: E.10, 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 EDO.8: 3 residues within 4Å: Chain B: E.113, E.114, D.116 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.115 Water bridges: B:E.114, B:D.116

2 x NP8: 5-(5-methoxypyridin-3-yl)-3-methyl-8-[(piperidin-4-yl)amino]-1,2-dihydro-1,7-naphthyridin-2-one(Non-covalent)

NP8.3: 10 residues within 4Å: Chain A: V.30, V.35, D.36, E.39, V.40, Y.85, N.86, D.90, D.93, I.96 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:V.40 Hydrogen bonds: A:D.36, A:N.86, A:N.86, A:N.86, A:D.93 NP8.9: 10 residues within 4Å: Chain B: V.30, V.35, D.36, E.39, V.40, Y.85, N.86, D.90, D.93, I.96 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.30, B:V.35, B:V.40 Hydrogen bonds: B:D.36, B:E.39, B:N.86, B:N.86, B:N.86, B:D.93

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

SO4.4: 2 residues within 4Å: Chain A: L.95, R.99 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.99, 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:H.63 Salt bridges: A:R.9, A:R.12, A:R.16 SO4.6: 4 residues within 4Å: Chain A: Q.49, K.59 Chain B: K.64 Ligands: SO4.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:K.59, A:K.59 Salt bridges: B:K.59, B:K.64, A:K.59 SO4.10: 2 residues within 4Å: Chain B: L.95, R.99 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.99, B:R.99 Salt bridges: B:R.99 SO4.11: 3 residues within 4Å: Chain B: R.9, R.12, R.16 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.12, B:R.16, B:H.63 Salt bridges: B:R.9, B:R.12, B:R.16 SO4.12: 4 residues within 4Å: Chain A: K.64 Chain B: Q.49, K.59 Ligands: SO4.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:K.59, B:K.59 Salt bridges: A:K.59, A:K.64, B:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demont, E.H. et al., Fragment-Based Discovery of Low-Micromolar Atad2 Bromodomain Inhibitors. J.Med.Chem. (2015)

Release Date

2015-07-22

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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