Research workbench
Aminopyrrolidine factor xa inhibitor
Analyse Aminopyrrolidine factor xa inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VVC
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated factor xa heavy chain; Factor X light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- LZF, NA, CA
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 36% strand | P00742 |
| B | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 225 | 14% helix, 38% strand | P00742 |
| K | Factor X light chain (EC 3.4.21.6) | protein | 53 | 8% helix, 30% strand | P00742 |
| L | Factor X light chain (EC 3.4.21.6) | protein | 52 | 8% helix, 27% strand | P00742 |
Ligands and binding sites
- LZF · 5-chloro-N-[(3S,4S)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-4-methoxypyrrolidin-3-yl]thiophene-2-carboxamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.54 | 0.76 | 39 | LZF |
| 2 | 121 | 0.47 | 0.79 | 31 | LZF |
| 3 | 118 | 0.45 | 0.78 | 28 | empty |
| 4 | 104 | 0.45 | 0.79 | 26 | empty |
| 5 | 151 | 0.44 | 0.75 | 29 | empty |
Interfaces
4 interfaces between chains.
- B–K · 937 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 882 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 183 Ų buried · 5 hydrogen bonds · protein-protein
- A–K · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 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 2VVC · PDBe 2VVC · UniProt P00742
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