Research workbench
Small molecule inhibitors of the ledgf site of HIV integrase identified by fragment screening and structure based design.
Analyse Small molecule inhibitors of the ledgf site of HIV integrase identified by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZCM
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV integrase
- EC
- 2.7.7.-
- UniProt
- Q76353
- Ligands
- PX3, 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 | HIV integrase (EC 2.7.7.-) | protein | 149 | 53% helix, 21% strand | Q76353 |
Ligands and binding sites
- PX3 · 5-[[[2-[(4-methoxyphenyl)methylcarbamoyl]phenyl]methyl-prop-2-enyl-amino]methyl]-1,3-benzodioxole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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 | 233 | 0.64 | 0.82 | 28 | SO4, ACT |
| 2 | 92 | 0.47 | 0.81 | 20 | empty |
| 3 | 112 | 0.46 | 0.78 | 17 | PX3 |
| 4 | 84 | 0.45 | 0.80 | 20 | empty |
| 5 | 123 | 0.43 | 0.76 | 17 | PX3 |
Interfaces
1 interface between chains.
- A–B · 1493 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3ZCM · Small molecule inhibitors of the LEDGF site of HIV integrase identified by fragment… · 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 3ZCM · PDBe 3ZCM · UniProt Q76353
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