MolNFT v1 · #56408 · protein
Potent, nonpeptide inhibitors of human mast cell tryptase
2ZEB · Tryptase beta 2: “Potent, nonpeptide inhibitors of human mast cell tryptase”. X-ray diffraction, 1 ligand (11M), 9 pockets (best druggability 0.53). MolNFT v1 #56408 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZEB
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptase beta 2
- EC
- 3.4.21.-
- UniProt
- Q6B052
- Ligands
- 11M
- Pockets
- 9 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tryptase beta 2 (EC 3.4.21.-) | protein | 242 | 10% helix, 35% strand | Q6B052 |
Ligands and binding sites
- 11M · 1-(1'-{[3-(methylsulfanyl)-2-benzothiophen-1-yl]carbonyl}spiro[1-benzofuran-3,4'-piperidin]-5-yl)methanamine · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.53 | 0.76 | 31 | empty |
| 2 | 248 | 0.53 | 0.76 | 32 | empty |
| 3 | 263 | 0.49 | 0.74 | 57 | 11M |
| 4 | 80 | 0.38 | 0.78 | 21 | 11M |
| 5 | 80 | 0.37 | 0.77 | 23 | 11M |
Interfaces
4 interfaces between chains.
- A–C · 1121 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1091 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 386 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2ZEB · Potent, Nonpeptide Inhibitors of Human Mast Cell Tryptase · 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 Q6B052
- Elsewhere: RCSB PDB 2ZEB · PDBe 2ZEB · UniProt Q6B052
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