MolNFT v1 · #98220 · protein
Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4- FLUOROPHENYL)SULFONYL-2-methylbenzimidazole
4L2O · Aldehyde dehydrogenase: “Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4…”. X-ray diffraction, 3 ligands (NAD, 1DD, K), 15 pockets (best druggability 0.84). MolNFT v1 #98220 on GenesisL1: 3D structure, binding…
- PDB
- 4L2O
- Type
- protein
- Length
- 1,787 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.5
- UniProt
- P30838
- Ligands
- NAD, 1DD, K
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.5) | protein | 446 | 45% helix, 17% strand | P30838 |
| B, E, G | Aldehyde dehydrogenase (EC 1.2.1.5) | protein | 447 | 46% helix, 17% strand | P30838 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, E, G
- 1DD · 1-[(4-fluorophenyl)sulfonyl]-2-methyl-1H-benzimidazole · ligand · 4 copies · chains A, B, E, G
- K · Potassium ion · metal · 7 copies · chains A, B, E, G
- ACT · Acetate ion · additive · 4 copies · chains A, B, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.84 | 0.86 | 108 | empty |
| 2 | 1168 | 0.83 | 0.85 | 125 | empty |
| 3 | 377 | 0.74 | 0.84 | 39 | 1DD |
| 4 | 346 | 0.73 | 0.84 | 38 | 1DD |
| 5 | 345 | 0.73 | 0.84 | 42 | 1DD |
Interfaces
4 interfaces between chains.
- E–G · 4023 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 3994 Ų buried · 79 hydrogen bonds · protein-protein
- B–G · 39 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4L2O · Crystal structure of human ALDH3A1 with its selective inhibitor… · the same entry in another collection · chain G against G, TM-score 1.00
- P30838 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, dimeric NADP-preferring… · a predicted model of the same protein · chain B 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 P30838
- Elsewhere: RCSB PDB 4L2O · PDBe 4L2O · UniProt P30838
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