Research workbench
Structure and property based design of factor xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs
Analyse Structure and property based design of factor xa inhibitors: pyrrolidin-2-ones… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y82
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- 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
- 930, CA, MG
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated factor xa heavy chain (EC 3.4.21.6) | protein | 234 | 14% helix, 36% strand | P00742 |
| B | Factor X light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- 930 · 6-chloro-N-((3S)-2-oxo-1-{4-[(2S)-2-pyrrolidinyl]phenyl}-3-pyrrolidinyl)-2-naphthalenesulfonamide · ligand · chains A
- CA · Calcium ion · metal · chains A
- MG · Magnesium 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 | 156 | 0.45 | 0.76 | 27 | empty |
| 2 | 110 | 0.43 | 0.77 | 26 | 930 |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2Y82 · Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00742 · AlphaFold monomer V2.0 prediction for coagulation factor X (P00742) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2Y82 · PDBe 2Y82 · UniProt P00742
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