Research workbench
Orally active thrombin inhibitors in complex with thrombin INH12
Analyse Orally active thrombin inhibitors in complex with thrombin INH12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A2X
- Type
- protein
- Length
- 294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Synthetic peptide
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NA9
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain | protein | 34 | 26% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| P | Synthetic peptide | protein | 10 | 30% helix, 0% strand | — |
Ligands and binding sites
- NA9 · N-(carboxymethyl)-3-cyclohexyl-D-alanyl-N-({6-[amino(imino)methyl]pyridin-3-yl}methyl)-N~2~-methyl-L-alaninamide · ligand · chains H
- SIN · Succinic acid · additive · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.56 | 0.77 | 37 | NA9 |
| 2 | 64 | 0.36 | 0.78 | 19 | empty |
| 3 | 59 | 0.35 | 0.77 | 14 | empty |
| 4 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1349 Ų buried · 28 hydrogen bonds · protein-protein
- H–P · 701 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, additive adduct, hydroxylation).
Compared structures
- 2A2X · Orally Active Thrombin Inhibitors in Complex with Thrombin Inh12 · 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 2A2X · PDBe 2A2X · UniProt P00734
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