MolNFT v1 · #143637 · protein

ALDH1A2 liganded with 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4- (METHYLSULFONYL)PHENYL]-1H-pyrazole-4-carboxamide (compound CM121)

6B5I · Retinal dehydrogenase 2: “ALDH1A2 liganded with 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4…”. X-ray diffraction, 1 ligand (CU4), 20 pockets (best druggability 0.90). MolNFT v1 #143637 on GenesisL1: 3D structure, binding sites and…

PDB: 6B5I
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: CU4
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% 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, 22% strand	O94788

Ligands and binding sites

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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	833	0.90	0.93	78	empty
2	272	0.83	0.94	33	empty
3	125	0.79	0.98	27	empty
4	124	0.79	0.98	31	empty
5	514	0.78	0.85	69	empty

Interfaces

6 interfaces between chains.

B–D · 2834 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 2812 Å² buried · 56 hydrogen bonds · protein-protein
C–D · 1651 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1588 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 1033 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6B5I · ALDH1A2 liganded with 1-(4-cyanophenyl)-N-(3-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]-1H… · 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 6B5I · PDBe 6B5I · UniProt O94788

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