Research workbench
Crystal structure of human heparanase in complex with covalent inhibitor VB151
Analyse Crystal structure of human heparanase in complex with covalent inhibitor VB151 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B0B
- Type
- protein
- Length
- 457 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Homo sapiens
- Molecule
- Heparanase 50 kDa subunit; Heparanase 8 kDa subunit
- UniProt
- Q9Y251
- Ligands
- OUU, NAG
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Heparanase 50 kDa subunit | protein | 384 | 32% helix, 26% strand | Q9Y251 |
| BBB | Heparanase 8 kDa subunit | protein | 73 | 34% helix, 29% strand | Q9Y251 |
Ligands and binding sites
- OUU · (1~{S},2~{R},3~{R},4~{S},6~{S})-2-(2-acetamidoethoxy)-3,4,6-tris(oxidanyl)cyclohexane-1-carboxylic acid · ligand · chains AAA, BBB
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains AAA
- EDO · 1,2-ethanediol · additive · chains AAA
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.46 | 0.80 | 25 | empty |
| 2 | 146 | 0.43 | 0.75 | 35 | OUU |
| 3 | 95 | 0.41 | 0.77 | 22 | EDO |
| 4 | 51 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- AAA–BBB · 4262 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- Q9Y251 · AlphaFold monomer V2.0 prediction for heparanase (Q9Y251) · a predicted model of the same protein · chain AAA 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 Q9Y251
- Elsewhere: RCSB PDB 8B0B · PDBe 8B0B · UniProt Q9Y251
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