9R8Q image
Deposition Date 2025-05-16
Release Date 2025-06-18
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9R8Q
Keywords:
Title:
Structure of thrombin bound to BAY 3389934
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Hirudo medicinalis (Taxon ID: 6421)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Prothrombin
Gene (Uniprot):F2
Chain IDs:B (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hirudin-2
Chain IDs:C (auth: I)
Chain Length:11
Number of Molecules:1
Biological Source:Hirudo medicinalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Prothrombin
Gene (Uniprot):F2
Chain IDs:A (auth: L)
Chain Length:29
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TYS C TYR modified residue
Primary Citation
Discovery of BAY 3389934 Hydrochloride: A Potent and Selective Small-Molecule Dual Factor IIa/Xa Inhibitor with Short Half-Life for the Acute Treatment of Sepsis-Induced Coagulopathy.
J.Med.Chem. 68 12687 12707 (2025)
PMID: 40498640 DOI: 10.1021/acs.jmedchem.5c00538

Abstact

Sepsis-induced coagulopathy (SIC) is a severe and frequent complication of sepsis, which is associated with high mortality in patients. So far, attempts have failed to establish a global standard of care in this difficult-to-treat indication. Anticoagulation with a dual inhibitor of the coagulation factors IIa (FIIa, thrombin) and Xa (FXa) has the potential to improve the treatment of life-threatening acute coagulation disorders, such as SIC. Herein, we describe the discovery of BAY 3389934 hydrochloride (31), a potent and highly selective, direct dual FIIa/Xa inhibitor, with high solubility suited for i.v. application. This small molecule acts as a metabolically soft active pharmaceutical ingredient (API) due to a labile carboxylic ester group, which is responsible for the desired short pharmacokinetic and pharmacological half-life (t1/2), resulting in a high controllability of the pharmacological action.

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Primary Citation of related structures