SMTL ID : 4qst.2 (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

homo-dimer

Ligands

2 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 12Q.19: 8 residues within 4Å: Chain B: V.30, V.35, E.39, V.40, Y.43, Y.85, N.86, I.96 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.30, B:V.35, B:Y.85 Hydrogen bonds: B:N.86

4 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: 4 residues within 4Å: Chain A: K.59, K.64 Chain B: K.64 Ligands: SO4.21 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Water bridges: B:K.59, B:K.59, B:K.64, B:K.64, A:K.59, A:K.59, A:K.59 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64 SO4.20: 4 residues within 4Å: Chain B: R.9, R.12, R.16 Ligands: EDO.23 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 SO4.21: 4 residues within 4Å: Chain A: K.64 Chain B: K.59, K.64 Ligands: SO4.3 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Water bridges: B:K.59, B:K.59, A:K.59, A:K.59, A:K.64, A:K.64, A:K.64 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64

30 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 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: M.2, E.5, D.6, R.9 Ligands: SO4.2 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: K.26, R.29, R.99 Ligands: EDO.16 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: I.111, K.112, L.115 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: H.20, A.23, I.24 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: P.34, S.54, S.55, S.58 Ligands: EDO.18 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain A: H.20 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: D.61, L.62, H.63 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: P.87, D.88, R.89, R.94, R.97 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.94, H.98 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: F.8, R.12, H.63, L.66, R.130 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: D.76, C.79, L.83, R.104 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: R.99 Ligands: EDO.6 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: R.104, D.105, Y.108 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: P.34, P.50, D.52, S.55 Ligands: EDO.9 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: E.10, E.114, L.115, D.116, F.119 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: M.2, E.5, D.6, R.9 Ligands: SO4.20 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: K.26, R.29, R.99 Ligands: EDO.34 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: I.111, K.112, L.115 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: H.20, A.23, I.24 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: P.34, S.54, S.55, S.58 Ligands: EDO.36 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain B: H.20 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: D.61, L.62, H.63 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: P.87, D.88, R.89, R.94, R.97 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: R.94, H.98 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: F.8, R.12, H.63, L.66, R.130 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: D.76, C.79, L.83, R.104 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain B: R.99 Ligands: EDO.24 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: R.104, D.105, Y.108 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: P.34, P.50, D.52, S.55 Ligands: EDO.27 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ATPase family AAA domain-containing protein 2

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