Research workbench
Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification
Analyse Parallel screening of a low molecular weight compound library: do differences… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AH9
- Type
- protein
- Length
- 304 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
- 0MB, TAM, SO4, CL
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.1) | protein | 154 | 50% helix, 22% strand | P12497 |
| B | Integrase (EC 2.7.7.1) | protein | 150 | 50% helix, 21% strand | P12497 |
Ligands and binding sites
- 0MB · 1-(3-phenyl-1,2,4-thiadiazol-5-yl)-1,4-diazepane · ligand · 2 copies · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- GOL · Glycerol · 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 | 147 | 0.51 | 0.79 | 26 | 0MB, EDO |
| 2 | 204 | 0.48 | 0.75 | 36 | EDO |
| 3 | 140 | 0.48 | 0.77 | 18 | EDO, CL, SO4 |
| 4 | 118 | 0.48 | 0.79 | 26 | 0MB, EDO |
| 5 | 129 | 0.47 | 0.78 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4AH9 · 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 4AH9 · PDBe 4AH9 · UniProt P12497
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