MolNFT v1 · #134766 · protein

Crystal structure of HIV-1 reverse transcriptase in complex with 5- chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY) phenoxy)-8-methyl-2-naphthonitrile (JLJ651), a non-nucleoside inhibitor

5TER · HIV-1 reverse transcriptase, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase in complex with 5…”. X-ray diffraction, 3 ligands (7AY, MG, SO4), 14 pockets (best druggability 0.78). MolNFT v1 #134766 on GenesisL1: 3D…

PDB: 5TER
Type: protein
Length: 948 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, 2.7.7.-, 3.1.-.-
UniProt: P03366
Ligands: 7AY, MG, SO4
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% 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, 2.7.7.-, 3.1.-.-)	protein	547	31% 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, 2.7.7.-, 3.1.-.-)	protein	401	35% helix, 20% strand	P03366

Ligands and binding sites

7AY · 5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile · ligand · chains A
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	725	0.78	0.82	59	empty
2	266	0.73	0.86	32	7AY
3	444	0.70	0.81	52	empty
4	374	0.69	0.82	52	empty
5	547	0.68	0.78	48	empty

Interfaces

1 interface between chains.

A–B · 2755 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5TER · Crystal Structure of HIV-1 Reverse Transcriptase in Complex with… · 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 P03366
Elsewhere: RCSB PDB 5TER · PDBe 5TER · UniProt P03366

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