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Reduced quinone reductase 2 in complex with chloroquine

Analyse Reduced quinone reductase 2 in complex with chloroquine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FGL
Type: protein
Length: 923 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosyldihydronicotinamide dehydrogenase [quinone]
EC: 1.10.99.2
UniProt: P16083
Ligands: CLQ, FAD, ZN
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2)	protein	230	40% helix, 16% strand	P16083
D	Ribosyldihydronicotinamide dehydrogenase [quinone] (EC 1.10.99.2)	protein	233	39% helix, 16% strand	P16083

Ligands and binding sites

CLQ · N4-(7-chloro-quinolin-4-yl)-N1,N1-diethyl-pentane-1,4-diamine · ligand · 5 copies · chains A, B, C, D
FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc 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

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	495	0.79	0.86	42	FAD, CLQ
2	575	0.79	0.84	49	FAD, CLQ
3	468	0.78	0.86	52	empty
4	519	0.77	0.84	41	FAD, CLQ
5	615	0.76	0.82	52	FAD, CLQ

Interfaces

5 interfaces between chains.

C–D · 2076 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2057 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 863 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 134 Å² buried · 1 hydrogen bond · protein-protein
B–C · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4FGL · Reduced qui reductase 2 in complex with chloroquine · the same entry in another collection · chain A 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 P16083
Elsewhere: RCSB PDB 4FGL · PDBe 4FGL · UniProt P16083

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