MolNFT v1 · #47791 · protein
Factor xa in complex with the inhibitor 5-chloro-N-(2-(4-(2- oxopyridin-1(2H)-YL)BENZAMIDO)ETHYL)THIOPHENE-2-carboxamide
2P93: “Factor xa in complex with the inhibitor 5-chloro-N-(2-(4-(2…”. X-ray diffraction, 1 ligand (ME1), 2 pockets (best druggability 0.49). MolNFT v1 #47791 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2P93
- 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
- ME1
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor xa (EC 3.4.21.6) | protein | 234 | 14% helix, 37% strand | P00742 |
| L | Factor xa (EC 3.4.21.6) | protein | 52 | 13% helix, 27% strand | P00742 |
Ligands and binding sites
- ME1 · 5-chloro-N-(2-(4-(2-oxopyridin-1(2H)-yl)benzamido)ethyl)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 | 151 | 0.49 | 0.78 | 26 | ME1 |
| 2 | 148 | 0.46 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–L · 918 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2P93 · Factor xa in complex with the inhibitor 5-chloro-N-(2-(4-(2-oxopyridin-1(2H)-yl)benzamido)… · 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 2P93 · PDBe 2P93 · UniProt P00742
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