MolNFT v1 · #84715 · protein
Small molecule inhibitors of the ledgf site of HIV type 1 integrase identified by fragment screening and structure based drug design
3ZT4: “Small molecule inhibitors of the ledgf site of HIV type 1 integrase identified by fragment screening and…”. X-ray diffraction, 2 ligands (ZT2, SO4), 7 pockets (best druggability 0.52). MolNFT v1 #84715 on GenesisL1: 3D structure…
- PDB
- 3ZT4
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- ZT2, SO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 151 | 52% helix, 20% strand | Q76353 |
| B | Integrase (EC 2.7.7.-) | protein | 150 | 55% helix, 21% strand | Q76353 |
Ligands and binding sites
- ZT2 · 5-[(E)-(2-oxo-2,3-dihydro-1H-inden-1-ylidene)methyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.52 | 0.82 | 24 | ZT2 |
| 2 | 158 | 0.51 | 0.79 | 27 | ZT2 |
| 3 | 164 | 0.50 | 0.77 | 21 | empty |
| 4 | 114 | 0.49 | 0.79 | 17 | ZT2 |
| 5 | 198 | 0.46 | 0.74 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1525 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3ZT4 · Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by… · 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 Q76353
- Elsewhere: RCSB PDB 3ZT4 · PDBe 3ZT4 · UniProt Q76353
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