MolNFT v1 · #169242 · protein
Discovery of hydroxy pyrimidine factor ixa inhibitors
6X5J · Coagulation factor IX: “Discovery of hydroxy pyrimidine factor ixa inhibitors”. X-ray diffraction, 2 ligands (6NH, NA), 2 pockets (best druggability 0.54). MolNFT v1 #169242 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6X5J
- Type
- protein
- Length
- 284 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
- 6NH, NA
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor IX (EC 3.4.21.22) | protein | 234 | 12% helix, 38% strand | P00740 |
| B | Coagulation factor IX (EC 3.4.21.22) | protein | 50 | 8% helix, 24% strand | P00740 |
Ligands and binding sites
- 6NH · 2-(4-hydroxy-5-phenyl-1H-pyrazol-3-yl)-1H-benzoimidazole-5-carboxamidine · ligand · chains A
- NA · Sodium ion · metal · chains A
- CIT · Citric acid · additive · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.54 | 0.79 | 22 | empty |
| 2 | 141 | 0.48 | 0.78 | 31 | 6NH, CIT |
Interfaces
1 interface between chains.
- A–B · 814 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 6X5J · PDBe 6X5J · UniProt P00740
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