MolNFT v1 · #29702 · protein
Thrombin in complex with an oxazolopyridine inhibitor 2
1ZGV: “Thrombin in complex with an oxazolopyridine inhibitor 2”. X-ray diffraction, 1 ligand (501), 2 pockets (best druggability 0.54). MolNFT v1 #29702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZGV
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28511
- Ligands
- 501
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 276 | 17% helix, 32% strand | P00734 |
| B | Hirudin | protein | 10 | 0% helix, 0% strand | P28511 |
Ligands and binding sites
- 501 · N7-butyl-N2-(5-chloro-2-methylphenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidine-2,7-diamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.54 | 0.76 | 38 | 501 |
| 2 | 50 | 0.31 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P00734
- Every structure of UniProt P28511
- Elsewhere: RCSB PDB 1ZGV · PDBe 1ZGV · UniProt P00734 · UniProt P28511
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