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The crystal structure of human S-adenosylhomocysteine hydrolase (ahcy) bound to oxadiazole inhibitor
Analyse The crystal structure of human S-adenosylhomocysteine hydrolase (ahcy) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W49
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P23526
- Ligands
- NAD, 9W1
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 429 | 44% helix, 17% strand | P23526 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 9W1 · (4-amino-1,2,5-oxadiazol-3-yl)[(3R)-3-{4-[(3-methoxyphenyl)amino]-6-methylpyridin-2-yl}pyrrolidin-1-yl]methanone · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.80 | 0.89 | 33 | empty |
| 2 | 1084 | 0.79 | 0.81 | 85 | NAD, EDO, 9W1 |
| 3 | 1062 | 0.79 | 0.81 | 83 | NAD, EDO, 9W1 |
| 4 | 145 | 0.53 | 0.80 | 26 | empty |
| 5 | 93 | 0.40 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2998 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5W49 · The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P23526 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P23526) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P23526
- Elsewhere: RCSB PDB 5W49 · PDBe 5W49 · UniProt P23526
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