MolNFT v1 · #106336 · protein
Crystal structure of HIV-1 reverse transcriptase (Y181C) variant 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
4RW6 · Reverse TRANSCRIPTASE/RIBONUCLEASE H, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase (Y181C) variant in complex with…”. X-ray diffraction, 1 ligand (494), 11 pockets (best druggability 0.78). MolNFT v1 #106336 on…
- PDB
- 4RW6
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H, P66 subunit; Reverse TRANSCRIPTASE/RIBONUCLEASE H…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 494
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H, P66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 538 | 31% helix, 24% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H, P51 subunit (EC 2.7.7.49) | protein | 405 | 35% helix, 20% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.78 | 0.82 | 65 | empty |
| 2 | 1055 | 0.77 | 0.79 | 84 | 494 |
| 3 | 640 | 0.69 | 0.77 | 48 | empty |
| 4 | 459 | 0.68 | 0.79 | 60 | empty |
| 5 | 274 | 0.58 | 0.78 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 2704 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4RW6 · Crystal Structure of HIV-1 Reverse Transcriptase (Y181C) variant 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 4RW6 · PDBe 4RW6 · UniProt P03366
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