MolNFT v1 · #93511 · protein

Crystal structure of HIV-1 reverse transcriptase in complex with (E)- 3-(3-chloro-5-(4-chloro-2-(2-(2,4-dioxo-3,4- dihydropyrimidin-1(2H)- YL)ETHOXY)PHENOXY)PHENYL)ACRYLONITRILE (JLJ494), a non-nucleoside inhibitor

4H4M · Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H…: “Crystal structure of HIV-1 reverse transcriptase in complex with (E)…”. X-ray diffraction, 1 ligand (494), 18 pockets (best druggability 0.76). MolNFT v1 #93511 on…

PDB: 4H4M
Type: protein
Length: 976 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P66 rt; Reverse…
EC: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
UniProt: P03366
Ligands: 494
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P66 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	548	30% helix, 22% strand	P03366
B	Reverse TRANSCRIPTASE/RIBONUCLEASE H, exoribonuclease H, P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	428	32% helix, 18% strand	P03366

Ligands and binding sites

494 · (2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile · ligand · chains A
EDO · 1,2-ethanediol · additive

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

Pockets

18 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	901	0.76	0.79	73	empty
2	278	0.75	0.88	39	494
3	805	0.74	0.79	75	empty
4	296	0.67	0.82	33	empty
5	301	0.64	0.80	39	empty

Interfaces

1 interface between chains.

A–B · 2659 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

4H4M · 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 4H4M · PDBe 4H4M · UniProt P03366

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