MolNFT v1 · #85606 · protein
Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification
4AHS · Integrase: “Parallel screening of a low molecular weight compound library: do differences in methodology affect hit…”. X-ray diffraction, 2 ligands (AKH, SO4), 7 pockets (best druggability 0.55). MolNFT v1 #85606 on GenesisL1: 3D…
- PDB
- 4AHS
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase
- EC
- 2.7.7.1
- UniProt
- P12497
- Ligands
- AKH, SO4
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.1) | protein | 150 | 53% helix, 21% strand | P12497 |
| B | Integrase (EC 2.7.7.1) | protein | 151 | 52% helix, 21% strand | P12497 |
Ligands and binding sites
- AKH · 1-benzofuran-7-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.55 | 0.84 | 21 | AKH |
| 2 | 140 | 0.54 | 0.81 | 25 | AKH |
| 3 | 168 | 0.50 | 0.77 | 21 | ACT |
| 4 | 119 | 0.47 | 0.79 | 17 | EDO |
| 5 | 174 | 0.46 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1509 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4AHS · Parallel screening of a low molecular weight compound library: do differences in… · 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 P12497
- Elsewhere: RCSB PDB 4AHS · PDBe 4AHS · UniProt P12497
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