MolNFT v1 · #137783 · protein
HIV reverse transcriptase complexed with (E)-3-(pyrimidin-2-yl)-N-(5- (5,6,7,8-tetrahydronaphthalen-2-yl)-1H-pyrazol-3-YL)ACRYLAMIDE
5VZ6: “HIV reverse transcriptase complexed with (E)-3-(pyrimidin-2-yl)-N-(5…”. X-ray diffraction, 1 ligand (9TV), 17 pockets (best druggability 0.73). MolNFT v1 #137783 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VZ6
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV reverse transcriptase
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P04585
- Ligands
- 9TV
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV reverse transcriptase (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 554 | 32% helix, 24% strand | P04585 |
| B | HIV reverse transcriptase (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 400 | 39% helix, 19% strand | P04585 |
Ligands and binding sites
- 9TV · 3-(pyrimidin-2-yl)-N-[3-(5,6,7,8-tetrahydronaphthalen-2-yl)-1H-pyrazol-5-yl]propanamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.73 | 0.80 | 61 | empty |
| 2 | 566 | 0.71 | 0.79 | 47 | empty |
| 3 | 101 | 0.69 | 0.91 | 18 | 9TV |
| 4 | 241 | 0.66 | 0.83 | 37 | empty |
| 5 | 151 | 0.54 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2884 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5VZ6 · HIV Reverse Transcriptase complexed with (E)-3-(pyrimidin-2-yl)-N-(5-(5,6,7,8-tetrahydrona… · 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 P04585
- Elsewhere: RCSB PDB 5VZ6 · PDBe 5VZ6 · UniProt P04585
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