MolNFT v1 · #146851 · protein
ALDH1A1 N121S in complex with 6-{[(3-FLUOROPHENYL)METHYL]SULFANYL}-2- (oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-one (compound 13G)
6DUM · Retinal dehydrogenase 1: “ALDH1A1 N121S in complex with 6-{[(3-FLUOROPHENYL)METHYL]SULFANYL}-2…”. X-ray diffraction, 4 ligands (A5Y, NAI, YB), 4 pockets (best druggability 0.74). MolNFT v1 #146851 on GenesisL1: 3D structure, binding…
- PDB
- 6DUM
- Type
- protein
- Length
- 494 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal dehydrogenase 1
- EC
- 1.2.1.-, 1.2.1.36
- UniProt
- V9HW83
- Ligands
- A5Y, NAI, YB, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal dehydrogenase 1 (EC 1.2.1.-, 1.2.1.36) | protein | 494 | 41% helix, 22% strand | V9HW83 |
Ligands and binding sites
- A5Y · 6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- YB · Ytterbium (III) ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 7 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 | 616 | 0.74 | 0.81 | 65 | YB, A5Y, NAI, CL |
| 2 | 60 | 0.39 | 0.80 | 16 | empty |
| 3 | 73 | 0.37 | 0.77 | 15 | empty |
| 4 | 92 | 0.35 | 0.75 | 19 | empty |
Compared structures
- 6DUM · ALDH1A1 N121S in complex with 6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-pheny… · 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 6DUM · PDBe 6DUM · UniProt V9HW83
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