MolNFT v1 · #3988 · protein
Structure of thrombin complexed with selective non-electophilic inhibitors having cyclohexyl moieties at P1
1D9I: “Structure of thrombin complexed with selective non-electophilic inhibitors having cyclohexyl moieties at P1”. X-ray diffraction, 2 ligands (00P, NA), 3 pockets (best druggability 0.56). MolNFT v1 #3988 on GenesisL1: 3D structure…
- PDB
- 1D9I
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 00P, NA
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 279 | 14% helix, 32% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- 00P · (5S)-N-[(trans-4-aminocyclohexyl)methyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
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 | 0.56 | 0.76 | 42 | 00P |
| 2 | 52 | 0.29 | 0.75 | 17 | empty |
| 3 | 52 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–I · 627 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1D9I · Structure of thrombin complexed with selective non-electophilic inhibitors having… · the same entry in another collection · chain A against A, TM-score 1.00
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.42
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 1D9I · PDBe 1D9I · UniProt P00734 · UniProt P28504
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