MolNFT v1 · #27025 · protein
Porcine factor ixa complexed to 1-{3-[AMINO(IMINO) METHYL]PHENYL}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]- 3-(trifluoromethyl)-1H-pyrazole-5-carboxamide
1X7A · Coagulation factor ixa: “Porcine factor ixa complexed to 1-{3-[AMINO(IMINO) METHYL]PHENYL}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]…”. X-ray diffraction, 1 ligand (187), 4 pockets (best druggability 0.55). MolNFT v1 #27025 on…
- PDB
- 1X7A
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor ixa; Coagulation factor IX, light chain
- EC
- 3.4.21.22
- UniProt
- P16293
- Ligands
- 187
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Coagulation factor ixa (EC 3.4.21.22) | protein | 235 | 10% helix, 31% strand | P16293 |
| L | Coagulation factor IX, light chain | protein | 97 | 3% helix, 21% strand | P16293 |
Ligands and binding sites
- 187 · 1-{3-[amino(imino)methyl]phenyl}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.55 | 0.81 | 21 | empty |
| 2 | 87 | 0.40 | 0.77 | 18 | empty |
| 3 | 86 | 0.37 | 0.76 | 26 | 187 |
| 4 | 68 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- C–L · 760 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1X7A · Porcine Factor IXa Complexed to 1-{3-[amino(imino)methyl]phenyl}-N-[4-(1H-benzimidazol-1-y… · the same entry in another collection · chain C against C, TM-score 1.00
- P16293 · AlphaFold monomer V2.0 prediction for coagulation factor IX (P16293) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P16293
- Elsewhere: RCSB PDB 1X7A · PDBe 1X7A · UniProt P16293
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