Research workbench
Crystal structure of human ALDH1A1 bound to compound (R)-28
Analyse Crystal structure of human ALDH1A1 bound to compound (R)-28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JWU
- Type
- protein
- Length
- 494 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Retinal dehydrogenase 1
- UniProt
- V9HW83
- Ligands
- NAD, VMA, YB, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal dehydrogenase 1 | protein | 494 | 41% helix, 22% strand | V9HW83 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- VMA · 1-methyl-5-phenyl-6-{[(1R)-1-(pyridin-2-yl) ethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · chains A
- YB · Ytterbium (III) ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.75 | 0.82 | 68 | YB, NAD, VMA |
| 2 | 62 | 0.44 | 0.82 | 18 | empty |
| 3 | 72 | 0.38 | 0.78 | 15 | empty |
| 4 | 98 | 0.37 | 0.75 | 18 | empty |
Compared structures
- 7JWU · Crystal structure of human ALDH1A1 bound to compound (R)-28 · the same entry in another collection · chain A against A, TM-score 1.00
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 V9HW83
- Elsewhere: RCSB PDB 7JWU · PDBe 7JWU · UniProt V9HW83
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