MolNFT v1 · #114853 · protein

Crystal structure of HIV-1 reverse transcriptase in complex with 6- ((4-((4-CYANOPHENYL)AMINO)-1,3,5-triazin-2-YL)AMINO)-5,7-dimethyl-2- naphthonitrile (JLJ639), a non-nucleoside inhibitor

5C25 · HIV-1 reverse transcriptase, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase in complex with 6…”. X-ray diffraction, 3 ligands (639, MG, SO4), 15 pockets (best druggability 0.83). MolNFT v1 #114853 on GenesisL1: 3D…

PDB: 5C25
Type: protein
Length: 960 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
UniProt: P03366
Ligands: 639, MG, SO4
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 reverse transcriptase, P66 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	554	30% helix, 24% strand	P03366
B	HIV-1 reverse transcriptase, P51 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	406	35% helix, 20% strand	P03366

Ligands and binding sites

639 · 6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7- dimethyl-2-naphthonitrile · ligand · chains A, B
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.83	0.83	101	639
2	695	0.78	0.82	64	empty
3	204	0.67	0.85	28	empty
4	557	0.66	0.77	45	empty
5	235	0.62	0.81	33	empty

Interfaces

1 interface between chains.

A–B · 2664 Å² buried · 28 hydrogen bonds · protein-protein

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 P03366
Elsewhere: RCSB PDB 5C25 · PDBe 5C25 · UniProt P03366

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