Research workbench
Selective benzothiophine inhibitors of factor ixa
Analyse Selective benzothiophine inhibitors of factor ixa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LC5
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX
- EC
- 3.4.21.22
- UniProt
- P00740
- Ligands
- IZX, CA
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor IX (EC 3.4.21.22) | protein | 235 | 13% helix, 34% strand | P00740 |
| B | Coagulation factor IX (EC 3.4.21.22) | protein | 54 | 7% helix, 26% strand | P00740 |
Ligands and binding sites
- IZX · 1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine · ligand · chains A
- CA · Calcium ion · metal · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.48 | 0.77 | 20 | empty |
| 2 | 119 | 0.46 | 0.78 | 26 | IZX |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
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 P00740
- Elsewhere: RCSB PDB 3LC5 · PDBe 3LC5 · UniProt P00740
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