MolNFT v1 · #113323 · protein
Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor
5AC1 · Retinal dehydrogenase 1: “Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor”. X-ray diffraction, 3 ligands (K9P, TXE, MG), 20 pockets (best druggability 0.85). MolNFT v1 #113323 on GenesisL1: 3D structure, binding…
- PDB
- 5AC1
- Type
- protein
- Length
- 1,976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal dehydrogenase 1
- EC
- 1.2.1.36
- UniProt
- P51977
- Ligands
- K9P, TXE, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinal dehydrogenase 1 (EC 1.2.1.36) | protein | 494 | 40% helix, 21% strand | P51977 |
Ligands and binding sites
- K9P · 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one · ligand · 4 copies · chains A, B, C, D
- TXE · [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.85 | 0.90 | 58 | empty |
| 2 | 552 | 0.84 | 0.90 | 44 | empty |
| 3 | 709 | 0.79 | 0.83 | 71 | K9P, TXE, MG |
| 4 | 656 | 0.75 | 0.81 | 70 | K9P, TXE, MG |
| 5 | 679 | 0.75 | 0.80 | 71 | K9P, TXE, MG |
Interfaces
3 interfaces between chains.
- A–B · 2937 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2930 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5AC1 · Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P51977 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 1 (P51977) · a predicted model of the same protein · chain C 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 P51977
- Elsewhere: RCSB PDB 5AC1 · PDBe 5AC1 · UniProt P51977
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