MolNFT v1 · #24713 · protein
Factor xa in complex with the inhibitor 1-[6-methyl-4,5,6,7- TETRAHYDROTHIAZOLO(5,4-C)PYRIDIN-2-yl] carbonyl-2- carbamoyl-4-(6-chloronaphth-2-YLSULPHONYL)PIPERAZINE
1V3X · Coagulation factor X, heavy chain: “Factor xa in complex with the inhibitor 1-[6-methyl-4,5,6,7- TETRAHYDROTHIAZOLO(5,4-C)PYRIDIN-2-yl]…”. X-ray diffraction, 2 ligands (D76, CA), 2 pockets (best druggability 0.44). MolNFT v1 #24713…
- PDB
- 1V3X
- Type
- protein
- Length
- 285 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
- D76, CA
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X, heavy chain (EC 3.4.21.6) | protein | 233 | 13% helix, 38% strand | P00742 |
| B | Coagulation factor X, light chain (EC 3.4.21.6) | protein | 52 | 13% helix, 31% strand | P00742 |
Ligands and binding sites
- D76 · (2R)-4-[(6-chloro-2-naphthyl)sulfonyl]-1-[(5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl)carbonyl]piperaz ine-2-carboxamide · ligand · chains A
- CA · Calcium ion · metal · 2 copies · 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 | 88 | 0.44 | 0.80 | 22 | D76 |
| 2 | 89 | 0.40 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1V3X · Factor Xa in complex with the inhibitor 1-[6-methyl-4,5,6,7-tetrahydrothiazolo(5,4-c)pyrid… · 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 1V3X · PDBe 1V3X · UniProt P00742
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