Research workbench
Crystal structure of human aplha-thrombin in complex with BENZO[B]THIOPHENE inhibitor 3
Analyse Crystal structure of human aplha-thrombin in complex with BENZO[B]THIOPHENE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D3P
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- BT3, NAG, NA
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-thrombin (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
| B | Alpha-thrombin (EC 3.4.21.5) | protein | 250 | 14% helix, 35% strand | P00734 |
| H | Hirugen | protein | 12 | 25% helix, 0% strand | P28501 |
Ligands and binding sites
- BT3 · 3-[4-(2-pyrrolidin-1-yl-ethoxy)-benzyl]-2-4-(2-pyrrolidin-1-yl-ethoxy)-phenyl] -benzo[b]thiophen-6-ol · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains B
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 | 295 | 0.58 | 0.77 | 41 | BT3 |
| 2 | 51 | 0.30 | 0.76 | 20 | empty |
| 3 | 61 | 0.29 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1182 Ų buried · 27 hydrogen bonds · protein-protein
- B–H · 674 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 1D3P · Crystal structure of human aplha-thrombin in complex with BENZO[B]THIOPHENE inhibitor 3 · 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
- Every structure of UniProt P28501
- Elsewhere: RCSB PDB 1D3P · PDBe 1D3P · UniProt P00734 · UniProt P28501
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