MolNFT v1 · #84708 · protein
Small molecule inhibitors of the ledgf site of HIV type 1 integrase identified by fragment screening and structure based drug design
3ZSX: “Small molecule inhibitors of the ledgf site of HIV type 1 integrase identified by fragment screening and…”. X-ray diffraction, 2 ligands (N44, SO4), 7 pockets (best druggability 0.64). MolNFT v1 #84708 on GenesisL1: 3D structure…
- PDB
- 3ZSX
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- N44, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integrase (EC 2.7.7.-) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- N44 · 5-({[2-(benzylcarbamoyl)benzyl](prop-2-en-1-yl)amino}methyl)-1,3-benzodioxole-4-carboxylate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.64 | 0.82 | 28 | SO4, ACT |
| 2 | 85 | 0.47 | 0.81 | 20 | EDO |
| 3 | 96 | 0.46 | 0.80 | 22 | EDO |
| 4 | 114 | 0.46 | 0.78 | 17 | N44 |
| 5 | 162 | 0.45 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1500 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3ZSX · Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by… · the same entry in another collection · chain B against B, 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 3ZSX · PDBe 3ZSX · UniProt Q76353
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