SMTL ID : 4qss.2 (1 other biounit)

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with N-Methyl-2-pyrrolidone (NMP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.89, R.94 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.89, A:R.94 SO4.2: 5 residues within 4Å: Chain A: K.59 Chain B: K.59 Ligands: MPD.4, SO4.9, MPD.11 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Water bridges: B:Q.49, B:Q.49, B:K.59, B:K.59, B:K.59, A:Q.49, A:Q.49, A:K.59, A:K.59, A:K.59 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64 SO4.8: 2 residues within 4Å: Chain B: R.89, R.94 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.89, B:R.94 SO4.9: 5 residues within 4Å: Chain A: K.59 Chain B: K.59 Ligands: SO4.2, MPD.4, MPD.11 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Water bridges: B:Q.49, B:Q.49, B:K.59, B:K.59, B:K.59, A:Q.49, A:Q.49, A:K.59, A:K.59, A:K.59 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 Ligands: MPD.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.115 MPD.4: 8 residues within 4Å: Chain A: M.51, S.58, K.59, L.62 Chain B: K.48, P.50 Ligands: SO4.2, SO4.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.49 Hydrophobic interactions: A:K.59 MPD.5: 7 residues within 4Å: Chain A: E.10, F.14, E.114, L.115, D.116, F.119 Ligands: MPD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.14, A:L.115, A:D.116, A:F.119, A:F.119 Hydrogen bonds: A:E.10, A:D.116 MPD.10: 5 residues within 4Å: Chain B: E.113, E.114, L.115, D.116 Ligands: MPD.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.115 MPD.11: 8 residues within 4Å: Chain A: K.48, P.50 Chain B: M.51, S.58, K.59, L.62 Ligands: SO4.2, SO4.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.59 Water bridges: A:Q.49 MPD.12: 7 residues within 4Å: Chain B: E.10, F.14, E.114, L.115, D.116, F.119 Ligands: MPD.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.14, B:L.115, B:D.116, B:F.119, B:F.119 Hydrogen bonds: B:E.10, B:E.10, B:D.116

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: L.72, I.111, L.115 No protein-ligand interaction detected (PLIP) GOL.13: 3 residues within 4Å: Chain B: L.72, I.111, L.115 No protein-ligand interaction detected (PLIP)

2 x MB3: 1-methylpyrrolidin-2-one(Non-covalent)

MB3.7: 6 residues within 4Å: Chain A: V.30, V.35, Y.43, Y.85, N.86, I.96 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.85, A:I.96 Hydrogen bonds: A:N.86 MB3.14: 6 residues within 4Å: Chain B: V.30, V.35, Y.43, Y.85, N.86, I.96 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.85, B:I.96 Hydrogen bonds: B:N.86

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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