MolNFT v1 · #137954 · protein
The crystal structure of human S-adenosylhomocysteine hydrolase (ahcy) bound to benzothiazole inhibitor
5W4B · Adenosylhomocysteinase: “The crystal structure of human S-adenosylhomocysteine hydrolase (ahcy) bound to benzothiazole inhibitor”. X-ray diffraction, 2 ligands (NAD, 9W4), 20 pockets (best druggability 0.90). MolNFT v1 #137954 on…
- PDB
- 5W4B
- Type
- protein
- Length
- 2,570 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P23526
- Ligands
- NAD, 9W4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 428 | 44% helix, 17% strand | P23526 |
| B, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 429 | 42% helix, 17% strand | P23526 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- 9W4 · 4-[(2,5-dioxo-2,5-dihydro-1H-imidazol-1-yl)methyl]-N-[2-(morpholin-4-yl)-1,3-benzothiazol-6-yl]benzamide · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.90 | 0.91 | 95 | empty |
| 2 | 1061 | 0.83 | 0.84 | 107 | NAD, 9W4 |
| 3 | 1088 | 0.83 | 0.83 | 105 | NAD, 9W4 |
| 4 | 1183 | 0.82 | 0.84 | 114 | NAD, 9W4 |
| 5 | 1164 | 0.82 | 0.83 | 116 | NAD, 9W4 |
Interfaces
11 interfaces between chains.
- E–F · 3018 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3009 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1853 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1831 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 1814 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5W4B · The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to… · the same entry in another collection · chain F against F, TM-score 1.00
- P23526 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P23526) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 5W4B · PDBe 5W4B · UniProt P23526
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