MolNFT v1 · #59560 · protein
Crystal structure of thrombin in complex with inhibitor 15
3C1K · Prothrombin: “Crystal structure of thrombin in complex with inhibitor 15”. X-ray diffraction, 1 ligand (T15), 1 pocket (best druggability 0.54). MolNFT v1 #59560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3C1K
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28511
- Ligands
- T15
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 276 | 16% helix, 31% strand | P00734 |
| B | Hirugen | protein | 11 | 36% helix, 0% strand | P28511 |
Ligands and binding sites
- T15 · 2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide · ligand · chains A
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 | 272 | 0.54 | 0.76 | 42 | T15 |
Interfaces
1 interface between chains.
- A–B · 690 Ų buried · 10 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 3C1K · PDBe 3C1K · UniProt P00734 · UniProt P28511
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