Research workbench
Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R)-3-(CYCLOHEXYLMETHOXY)PIPERIDIN-4-yl-amino-3- methyl-1,2-dihydro-1,7-naphthyridin-2-one
Analyse Crystal structure of human ATAD2 bromodomain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A81
- Type
- protein
- Length
- 130 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase family aaa domain-containing protein 2
- EC
- 3.6.1.3
- UniProt
- Q6PL18
- Ligands
- 78J, SO4
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase family aaa domain-containing protein 2 (EC 3.6.1.3) | protein | 130 | 72% helix, 0% strand | Q6PL18 |
Ligands and binding sites
- 78J · (3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino}-3-methyl-1,2-dihydro-1,7-naphthyridin-2-one · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.48 | 0.80 | 21 | 78J |
Compared structures
- 5A81 · Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PL18 · AlphaFold monomer V2.0 prediction for ATPase family aaa domain- containing protein 2… · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6PL18
- Elsewhere: RCSB PDB 5A81 · PDBe 5A81 · UniProt Q6PL18
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