MolNFT v1 · #2704 · protein
Selective non electrophilic thrombin inhibitors with cyclohexyl moieties.
1C4V · THROMBIN:SHORT chain: “Selective non electrophilic thrombin inhibitors with cyclohexyl moieties.”. X-ray diffraction, 2 ligands (IH2, NA), 1 pocket (best druggability 0.57). MolNFT v1 #2704 on GenesisL1: 3D structure, binding sites…
- PDB
- 1C4V
- Type
- protein
- Length
- 298 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THROMBIN:SHORT chain; THROMBIN:LONG chain; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- IH2, NA
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | THROMBIN:SHORT chain (EC 3.4.21.5) | protein | 36 | 22% helix, 0% strand | P00734 |
| 2 | THROMBIN:LONG chain (EC 3.4.21.5) | protein | 252 | 15% helix, 33% strand | P00734 |
| 3 | Hirugen | protein | 10 | 30% helix, 0% strand | — |
Ligands and binding sites
- IH2 · 2-(2,2-diphenyl-ethyl)-7-methyl-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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.57 | 0.77 | 42 | IH2 |
Interfaces
2 interfaces between chains.
- 1–2 · 1477 Ų buried · 40 hydrogen bonds · protein-protein
- 2–3 · 637 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1C4V · Selective non electrophilic thrombin inhibitors with cyclohexyl moieties. · the same entry in another collection · chain 1 against 1, 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 1C4V · PDBe 1C4V · UniProt P00734
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