Research workbench
Crystal structure of human heparanase in complex with covalent inhibitor CB678
Analyse Crystal structure of human heparanase in complex with covalent inhibitor CB678 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PRT
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparanase 50 kda subunit; Heparanase 8 kda subunit
- UniProt
- Q9Y251
- Ligands
- 8I4, Z61, NAG, FUC, CL
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparanase 50 kda subunit | protein | 384 | 32% helix, 27% strand | Q9Y251 |
| B | Heparanase 8 kda subunit | protein | 74 | 32% helix, 32% strand | Q9Y251 |
Ligands and binding sites
- 8I4 · (2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid · ligand · chains A, B
- Z61 · 2-deoxy-alpha-D-arabino-hexopyranose · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
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 | 238 | 0.49 | 0.74 | 39 | 8I4, Z61, CL |
| 2 | 94 | 0.48 | 0.81 | 26 | EDO |
| 3 | 108 | 0.42 | 0.77 | 22 | EDO |
| 4 | 56 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4267 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 7PRT · Crystal structure of human heparanase in complex with covalent inhibitor CB678 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y251 · AlphaFold monomer V2.0 prediction for heparanase (Q9Y251) · a predicted model of the same protein · 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 Q9Y251
- Elsewhere: RCSB PDB 7PRT · PDBe 7PRT · UniProt Q9Y251
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