MolNFT v1 · #2886 · protein
Thrombin inhibitors with rigid tripeptidyl aldehydes
1CA8 · Thrombin light chain: “Thrombin inhibitors with rigid tripeptidyl aldehydes”. X-ray diffraction, 2 ligands (0KV, NA), 1 pocket (best druggability 0.52). MolNFT v1 #2886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1CA8
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0KV, NA
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 12% helix, 36% strand | P00734 |
| C | Hirugen | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 0KV · 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains B
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 | 0.52 | 0.76 | 38 | 0KV |
Interfaces
2 interfaces between chains.
- A–B · 1085 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1CA8 · Thrombin inhibitors with rigid tripeptidyl aldehydes · 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 P00734
- Elsewhere: RCSB PDB 1CA8 · PDBe 1CA8 · UniProt P00734
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