Research workbench
Selective non electrophilic thrombin inhibitors with cyclohexyl moieties.
Analyse Selective non electrophilic thrombin inhibitors with cyclohexyl moieties. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C4U
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Protein (hirugen)
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- IH1, NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Thrombin (EC 3.4.21.5) | protein | 30 | 33% helix, 0% strand | P00734 |
| 2 | Thrombin (EC 3.4.21.5) | protein | 252 | 15% helix, 35% strand | P00734 |
| 3 | Protein (hirugen) | protein | 8 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- IH1 · 2-[2-(4-bromo-benzenesulfonyl)-ethyl]-1-3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxylic acid(4-carbamimidoyl-cyclohexylmethyl)-amide · ligand · chains 2
- NA · Sodium ion · metal · chains 2
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 | 286 | 0.57 | 0.77 | 38 | IH1 |
| 2 | 68 | 0.32 | 0.75 | 13 | empty |
| 3 | 51 | 0.29 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- 1–2 · 1271 Ų buried · 28 hydrogen bonds · protein-protein
- 2–3 · 557 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P28504
- Elsewhere: RCSB PDB 1C4U · PDBe 1C4U · UniProt P00734 · UniProt P28504
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