Research workbench
Factor xa in complex with the inhibitor 5-chloro-N-((1R,2S)-2-(4-(2- oxopyridin-1(2H)-YL)BENZAMIDO) CYCLOPENTYL)THIOPHENE-2-carboxamide
Analyse Factor xa in complex with the inhibitor 5-chloro-N-((1R,2S)-2-(4-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P95
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor xa
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- ME5
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor xa (EC 3.4.21.6) | protein | 234 | 13% helix, 35% strand | P00742 |
| L | Factor xa (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- ME5 · 5-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-yl)benzamido) cyclopentyl)thiophene-2-carboxamide · ligand · 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 | 122 | 0.47 | 0.79 | 26 | ME5 |
| 2 | 127 | 0.44 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–L · 932 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2P95 · Factor xa in complex with the inhibitor 5-chloro-N-((1R,2S)-2-(4-(2-oxopyridin-1(2H)-YL)be… · 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 2P95 · PDBe 2P95 · UniProt P00742
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