Research workbench
Rapid development of two factor ixa inhibitors from hit to lead
Analyse Rapid development of two factor ixa inhibitors from hit to lead in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZU
- Type
- protein
- Length
- 292 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
- 4K6, NA, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor IX (EC 3.4.21.22) | protein | 235 | 13% helix, 37% strand | P00740 |
| B | Coagulation factor IX (EC 3.4.21.22) | protein | 57 | 7% helix, 25% strand | P00740 |
Ligands and binding sites
- 4K6 · N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 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 | 203 | 0.52 | 0.77 | 22 | empty |
| 2 | 96 | 0.49 | 0.82 | 24 | 4K6 |
| 3 | 68 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 7 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 4YZU · PDBe 4YZU · UniProt P00740
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