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Ternary complex of an orally active thrombin inhibitor with human thrombin and a C-terminal hirudin derived exo-sit inhibitor
Analyse Ternary complex of an orally active thrombin inhibitor with human thrombin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ANM
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- CDO
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| L | Thrombin (EC 3.4.21.5) | protein | 34 | 24% helix, 0% strand | P00734 |
Ligands and binding sites
- CDO · 2-((R)-1-((S)-2-(N-(6-carbamimidoylpyridin-3-yl)methylcarbamoyl)-2H-pyrrol-1(5H)-yl)-3-cyclohexyl-1-oxopropan-2-ylamino)acetic acid · ligand · chains H
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 | 254 | 0.55 | 0.77 | 36 | CDO |
| 2 | 58 | 0.37 | 0.79 | 14 | empty |
| 3 | 65 | 0.36 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- H–L · 1379 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ANM · Ternary complex of an orally active thrombin inhibitor with human thrombin and a… · the same entry in another collection · chain L against L, 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 2ANM · PDBe 2ANM · UniProt P00734
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