MolNFT v1 · #125171 · protein

Structure of ALDH2 in complex with 2P3

5L13 · Aldehyde dehydrogenase, mitochondrial: “Structure of ALDH2 in complex with 2P3”. X-ray diffraction, 3 ligands (GAI, 6ZE, NA), 20 pockets (best druggability 0.90). MolNFT v1 #125171 on GenesisL1: 3D structure, binding sites and…

PDB: 5L13
Type: protein
Length: 3,953 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase, mitochondrial
EC: 1.2.1.3
UniProt: P05091
Ligands: GAI, 6ZE, NA
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3)	protein	494	39% helix, 23% strand	P05091
E	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3)	protein	495	39% helix, 23% strand	P05091

Ligands and binding sites

GAI · Guanidine · ligand · 16 copies · chains A, B, C, D, E, F, G, H
6ZE · 2,3,5-trimethyl-6-propyl-7H-furo[3,2-g][1]benzopyran-7-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, D, C, E, F, H, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	894	0.90	0.93	73	empty
2	769	0.90	0.94	71	empty
3	430	0.85	0.93	40	empty
4	375	0.85	0.94	37	empty
5	178	0.82	0.97	39	EDO

Interfaces

14 interfaces between chains.

E–F · 2903 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2871 Å² buried · 49 hydrogen bonds · protein-protein
G–H · 2864 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 2861 Å² buried · 50 hydrogen bonds · protein-protein
E–H · 1629 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5L13 · Structure of ALDH2 in complex with 2P3 · the same entry in another collection · chain H against H, TM-score 1.00
P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain G 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 P05091
Elsewhere: RCSB PDB 5L13 · PDBe 5L13 · UniProt P05091

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