MolNFT v1 · #137515 · protein
Crystal structure of HIV-1 reverse transcriptase (K103N, Y181C) variant in complex with 2-chloro-N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4- dihydropyrimidin-1(2H)-YL)ETHOXY)PHENOXY)-4-methylnaphthalen-1-yl)-N- methylacetamide (JLJ686), a non-nucleoside inhibitor
5VQZ · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of HIV-1 reverse transcriptase (K103N, Y181C) variant in complex with…”. X-ray diffraction, 2 ligands (9HY, SO4), 16 pockets (best druggability 0.79). MolNFT v1 #137515 on…
- PDB
- 5VQZ
- Type
- protein
- Length
- 948 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- 9HY, SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 547 | 32% helix, 23% strand | P03366 |
| B | P51 rt | protein | 401 | 36% helix, 20% strand | P03366 |
Ligands and binding sites
- 9HY · N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylacetamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.79 | 0.80 | 81 | 9HY |
| 2 | 560 | 0.77 | 0.83 | 47 | empty |
| 3 | 605 | 0.66 | 0.76 | 46 | empty |
| 4 | 333 | 0.64 | 0.80 | 53 | empty |
| 5 | 320 | 0.62 | 0.79 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 2716 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VQZ · Crystal Structure of HIV-1 Reverse Transcriptase (K103N, 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 5VQZ · PDBe 5VQZ · UniProt P03366
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