Research workbench
Crystal structure of thrombin in complex with a novel bicyclic lactam inhibitor
Analyse Crystal structure of thrombin in complex with a novel bicyclic lactam inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JWT
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- BLI
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 299 | 14% helix, 29% strand | P00734 |
Ligands and binding sites
- BLI · 4-oxo-2-phenylmethanesulfonyl-octahydro-pyrrolo[1,2-a]pyrazine-6-carboxylic acid [1-(N-hydroxycarbamimidoyl)-piperidin-4-ylmethyl]-amide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.59 | 0.78 | 42 | BLI |
| 2 | 51 | 0.28 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1JWT · Crystal structure of thrombin in complex with a novel bicyclic lactam inhibitor · 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 1JWT · PDBe 1JWT · UniProt P00734
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