SMTL ID : 7ppx.1

ATAD2 in complex with FragLite3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.9, R.12, R.16 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.16, A:R.16 Salt bridges: A:R.9, A:R.12, A:R.16 SO4.16: 2 residues within 4Å: Chain A: K.59, K.64 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.59, A:K.59 Salt bridges: A:K.59, A:K.64

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.99 Ligand excluded by PLIP

1 x 7ZX: 4-bromanyl-1,2-oxazole(Non-covalent)

7ZX.3: 5 residues within 4Å: Chain A: K.59, K.64, D.70, R.73, D.74 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.59 pi-Stacking: A:Y.65

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

EDO.4: 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.5: 3 residues within 4Å: Chain A: H.20, A.23, I.57 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.23 EDO.6: 6 residues within 4Å: Chain A: V.68, K.69, L.72, I.111, L.115, E.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.120, A:E.120 EDO.7: 1 residues within 4Å: Chain A: H.20 No protein-ligand interaction detected (PLIP) EDO.8: 1 residues within 4Å: Chain A: R.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97 Water bridges: A:R.94 EDO.9: 3 residues within 4Å: Chain A: R.104, D.105, Y.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.105, A:D.105 EDO.10: 3 residues within 4Å: Chain A: H.63, L.66, R.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.63, A:R.130 Water bridges: A:R.12 EDO.11: 5 residues within 4Å: Chain A: P.34, D.52, S.54, S.55, S.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.52, A:S.58, A:S.58 EDO.12: 4 residues within 4Å: Chain A: D.105, T.106, A.109 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.102, A:T.106 EDO.13: 4 residues within 4Å: Chain A: A.109, I.110, E.113 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113, A:E.113 EDO.14: 3 residues within 4Å: Chain A: S.58, K.59, L.62 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: Q.121, E.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.121, A:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davison, G. et al., Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. J.Med.Chem. (2022)

Release Date

2022-09-21

Peptides

ATPase family AAA domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

ATPase family AAA domain-containing protein 2

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