MolNFT v1 · #33066 · protein
Thrombin inhibitors
2C8Y · Thrombin light chain: “Thrombin inhibitors”. X-ray diffraction, 2 ligands (C3M, NA), 3 pockets (best druggability 0.57). MolNFT v1 #33066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2C8Y
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- C3M, NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 34% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| I | Hirudin variant-2 | protein | 10 | 0% helix, 0% strand | P09945 |
Ligands and binding sites
- C3M · N-[(2R,3S)-3-amino-2-hydroxy-4-phenylbutyl]naphthalene-2-sulfonamide · ligand · chains B
- NA · Sodium ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.57 | 0.77 | 41 | DMS, C3M |
| 2 | 90 | 0.35 | 0.74 | 19 | empty |
| 3 | 51 | 0.32 | 0.77 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1189 Ų buried · 26 hydrogen bonds · protein-protein
- B–I · 637 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 2C8Y · thrombin inhibitors · 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
- Every structure of UniProt P09945
- Elsewhere: RCSB PDB 2C8Y · PDBe 2C8Y · UniProt P00734 · UniProt P09945
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