Research workbench
Factor xa in complex with the inhibitor apixaban (bms- 562247) aka 1-(4-methoxyphenyl)-7-oxo-6-(4-(2-oxo-1- PIPERIDINYL)PHENYL)-4,5,6,7-tetrahydro-1H-PYRAZOLO[3, 4- C]PYRIDINE-3-carboxamide
Analyse Factor xa in complex with the inhibitor apixaban (bms- 562247) aka… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P16
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X (ec 3.4.21.6) (stuart factor) (stuart-prower factor)
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- GG2, CA
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X (ec 3.4.21.6) (stuart factor) (stuart-prower factor) (EC 3.4.21.6) | protein | 234 | 13% helix, 36% strand | P00742 |
| L | Coagulation factor X (ec 3.4.21.6) (stuart factor) (stuart-prower factor) (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- GG2 · 1-(4-methoxyphenyl)-7-oxo-6-[4-(2-oxopiperidin-1-yl) phenyl]-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-c]pyridine-3-carboxamide · 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 | 169 | 0.50 | 0.77 | 29 | empty |
| 2 | 101 | 0.45 | 0.79 | 24 | GG2 |
Interfaces
1 interface between chains.
- A–L · 915 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 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 P00742
- Elsewhere: RCSB PDB 2P16 · PDBe 2P16 · UniProt P00742
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