SMTL ID : 4qst.1 (1 other biounit)

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 1-methylquinolin 2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x 12Q: 1-METHYLQUINOLIN-2(1H)-ONE(Non-covalent)

12Q.1: 8 residues within 4Å: Chain A: V.30, V.35, E.39, V.40, Y.43, Y.85, N.86, I.96 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:Y.85 Hydrogen bonds: A:N.86

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

SO4.2: 4 residues within 4Å: Chain A: R.9, R.12, R.16 Ligands: EDO.5 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 SO4.3: 2 residues within 4Å: Chain A: K.59, K.64 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.59, A:K.59, A:K.59, A:K.59, A:K.59 Salt bridges: A:K.59, A:K.64

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

EDO.4: 5 residues within 4Å: Chain A: E.10, 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 EDO.5: 5 residues within 4Å: Chain A: M.2, E.5, D.6, R.9 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.6 Water bridges: A:R.9 EDO.6: 4 residues within 4Å: Chain A: K.26, R.29, R.99 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.26 Water bridges: A:R.29 EDO.7: 3 residues within 4Å: Chain A: I.111, K.112, L.115 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: H.20, A.23, I.24 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.20, A:A.23 EDO.9: 5 residues within 4Å: Chain A: P.34, S.54, S.55, S.58 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.54, A:S.58 Water bridges: A:S.54 EDO.10: 1 residues within 4Å: Chain A: H.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.20 EDO.11: 3 residues within 4Å: Chain A: D.61, L.62, H.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.62 Water bridges: A:D.61 EDO.12: 5 residues within 4Å: Chain A: P.87, D.88, R.89, R.94, R.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.94, A:R.94, A:R.97 Water bridges: A:D.88, A:R.89 EDO.13: 2 residues within 4Å: Chain A: R.94, H.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.14: 5 residues within 4Å: Chain A: F.8, R.12, H.63, L.66, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.12 Water bridges: A:H.63 EDO.15: 4 residues within 4Å: Chain A: D.76, C.79, L.83, R.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.76, A:D.76, A:S.80 EDO.16: 2 residues within 4Å: Chain A: R.99 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99, A:R.99 EDO.17: 3 residues within 4Å: Chain A: R.104, D.105, Y.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:D.105 Water bridges: A:R.104 EDO.18: 5 residues within 4Å: Chain A: P.34, P.50, D.52, S.55 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.55 Water bridges: A:P.50, A:S.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain. MedChemComm (2014)

Release Date

2014-07-23

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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