MolNFT v1 · #52298 · protein
Aminopyrrolidine factor xa inhibitor
2VWM · Activated factor xa heavy chain: “Aminopyrrolidine factor xa inhibitor”. X-ray diffraction, 2 ligands (LZI, NA), 6 pockets (best druggability 0.51). MolNFT v1 #52298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VWM
- Type
- protein
- Length
- 562 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
- LZI, NA
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 232 | 14% helix, 37% 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, 26% strand | P00742 |
| L | Factor X light chain (EC 3.4.21.6) | protein | 52 | 8% helix, 31% strand | P00742 |
Ligands and binding sites
- LZI · (4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
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 | 238 | 0.51 | 0.75 | 37 | LZI |
| 2 | 84 | 0.45 | 0.80 | 20 | empty |
| 3 | 123 | 0.44 | 0.77 | 28 | empty |
| 4 | 136 | 0.44 | 0.76 | 25 | empty |
| 5 | 96 | 0.42 | 0.78 | 24 | LZI |
Interfaces
4 interfaces between chains.
- B–K · 907 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 877 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 191 Ų buried · 1 hydrogen bond · protein-protein
- A–K · 34 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 2VWM · PDBe 2VWM · UniProt P00742
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