MolNFT v1 · #84177 · protein
Small molecule inhibitors of the ledgf site of HIV integrase identified by fragment screening and structure based design.
3ZCM: “Small molecule inhibitors of the ledgf site of HIV integrase identified by fragment screening and structure…”. X-ray diffraction, 2 ligands (PX3, SO4), 7 pockets (best druggability 0.64). MolNFT v1 #84177 on GenesisL1: 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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