Research workbench

ALDH1A2 liganded with NAD and compound WIN18,446

Analyse ALDH1A2 liganded with NAD and compound WIN18,446 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ALJ
Type: protein
Length: 1,968 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase 1A2
EC: 1.2.1.36
UniProt: O94788
Ligands: NAD, CW2
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aldehyde dehydrogenase 1A2 (EC 1.2.1.36)	protein	492	40% helix, 22% strand	O94788

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
CW2 · N,N'-(octane-1,8-diyl)bis(2,2-dichloroacetamide) · 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1173	0.91	0.93	108	empty
2	209	0.79	0.93	37	empty
3	213	0.79	0.93	40	empty
4	233	0.78	0.92	45	empty
5	441	0.78	0.86	66	empty

Interfaces

6 interfaces between chains.

B–D · 2760 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 2759 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 1641 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1633 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 953 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

6ALJ · ALDH1A2 liganded with NAD and compound WIN18,446 · 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 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 O94788
Elsewhere: RCSB PDB 6ALJ · PDBe 6ALJ · UniProt O94788

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