MolNFT v1 · #21456 · protein
Novel non-covalent thrombin inhibitors incorporating P1 4,5,6,7- tetrahydrobenzothiazole arginine side chain mimetics
1SB1 · Prothrombin: “Novel non-covalent thrombin inhibitors incorporating P1 4,5,6,7- tetrahydrobenzothiazole arginine side chain…”. X-ray diffraction, 2 ligands (165, NA), 1 pocket (best druggability 0.53). MolNFT v1 #21456 on GenesisL1…
- PDB
- 1SB1
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 165, NA
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 35% strand | P00734 |
| I | Hirugen | protein | 9 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- 165 · N-(benzylsulfonyl)-3-cyclohexylalanyl-N-(2-amino-1,3-benzothiazol-6-yl)prolinamide · ligand · chains H
- NA · Sodium ion · metal · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.53 | 0.77 | 33 | 165 |
Interfaces
2 interfaces between chains.
- L–H · 1192 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 562 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1SB1 · Novel Non-Covalent Thrombin Inhibitors Incorporating P1 4,5,6,7-Tetrahydrobenzothiazole… · the same entry in another collection · chain L against L, TM-score 1.00
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.56
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 P28504
- Elsewhere: RCSB PDB 1SB1 · PDBe 1SB1 · UniProt P00734 · UniProt P28504
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