Research workbench
HIV-rt with non-nucleoside inhibitor annulated pyrazole 2
Analyse HIV-rt with non-nucleoside inhibitor annulated pyrazole 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E01
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- PZ2
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gag-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 552 | 32% helix, 22% strand | P04585 |
| B | Gag-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 401 | 39% helix, 18% strand | P04585 |
Ligands and binding sites
- PZ2 · 3-[2-bromo-4-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-methylbenzonitrile · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.80 | 0.82 | 95 | PZ2 |
| 2 | 263 | 0.70 | 0.85 | 40 | empty |
| 3 | 379 | 0.70 | 0.82 | 31 | empty |
| 4 | 207 | 0.55 | 0.79 | 32 | empty |
| 5 | 81 | 0.50 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2962 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3E01 · HIV-RT with non-nucleoside inhibitor annulated pyrazole 2 · 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 3E01 · PDBe 3E01 · UniProt P04585
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