SMTL ID : 7z9s.1

ATAD2 in complex with PepLite-Arg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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 SO4.10: 2 residues within 4Å: Chain A: K.59, K.64 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.49, 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 IJI: (2~{S})-2-acetamido-5-carbamimidamido-~{N}-prop-2-enyl-pentanamide(Covalent)

IJI.3: 4 residues within 4Å: Chain A: R.94, R.97, H.98, C.101 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.94, A:H.98 Hydrogen bonds: A:R.97 Water bridges: A:R.94, A:R.94

6 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.10, A:E.114, A:D.116 EDO.5: 2 residues within 4Å: Chain A: H.20, A.23 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: K.48, P.50 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: K.69, L.115, E.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.120, A:E.120 Water bridges: A:I.111 EDO.8: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.115 EDO.9: 2 residues within 4Å: Chain A: L.66, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130, A:R.130

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

2022-11-23

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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