MolNFT v1 · #143636 · protein
ALDH1A2 liganded with NAD and 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3- [4-(METHYLSULFONYL)PHENYL]-1H-pyrazole-4-carboxamide (compound CM121)
6B5H · Retinal dehydrogenase 2: “ALDH1A2 liganded with NAD and 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3…”. X-ray diffraction, 2 ligands (NAD, CU4), 20 pockets (best druggability 0.90). MolNFT v1 #143636 on GenesisL1: 3D structure, binding…
- PDB
- 6B5H
- Type
- protein
- Length
- 1,968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal dehydrogenase 2
- EC
- 1.2.1.36
- UniProt
- O94788
- Ligands
- NAD, CU4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinal dehydrogenase 2 (EC 1.2.1.36) | protein | 492 | 40% helix, 23% strand | O94788 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CU4 · 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]-1H-pyrazole-4-carboxamide · ligand · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.90 | 0.93 | 75 | empty |
| 2 | 345 | 0.84 | 0.94 | 32 | empty |
| 3 | 211 | 0.79 | 0.93 | 41 | empty |
| 4 | 487 | 0.78 | 0.86 | 68 | empty |
| 5 | 228 | 0.78 | 0.92 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2788 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2781 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1631 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1593 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 962 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6B5H · ALDH1A2 liganded with NAD and 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4-(methylsulfonyl)ph… · the same entry in another collection · chain D against D, TM-score 1.00
- O94788 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 2 (O94788) · a predicted model of the same protein · chain D 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 O94788
- Elsewhere: RCSB PDB 6B5H · PDBe 6B5H · UniProt O94788
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