MolNFT v1 · #59996 · protein
Factor xa in complex with the inhibitor N-(2-(((5-chloro-2- pyridinyl) AMINO)SULFONYL)PHENYL)-4-(2-oxo-1(2H)- PYRIDINYL)BENZAMIDE
3CEN · Coagulation factor X, heavy chain: “Factor xa in complex with the inhibitor N-(2-(((5-chloro-2- pyridinyl) AMINO)SULFONYL)PHENYL)-4-(2-oxo-1(2H)…”. X-ray diffraction, 1 ligand (FXA), 2 pockets (best druggability 0.49). MolNFT v1…
- PDB
- 3CEN
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X, heavy chain; Coagulation factor X, light chain
- EC
- 3.4.21.6
- UniProt
- P00742
- Ligands
- FXA
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X, heavy chain (EC 3.4.21.6) | protein | 234 | 13% helix, 36% strand | P00742 |
| L | Coagulation factor X, light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 27% strand | P00742 |
Ligands and binding sites
- FXA · N-(2-(((5-chloro-2-pyridinyl)amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide · 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 | 135 | 0.49 | 0.79 | 26 | FXA |
| 2 | 84 | 0.36 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–L · 969 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3CEN · Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl)… · the same entry in another collection · chain L against L, 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 3CEN · PDBe 3CEN · UniProt P00742
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