9R8Q | pdb_00009r8q

Structure of thrombin bound to BAY 3389934

PDB DOI: https://doi.org/10.2210/pdb9R8Q/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Hirudo medicinalis
Expression System: Bos taurus, synthetic construct
Mutation(s): No

Deposited: 2025-05-16 Released: 2025-06-18
Deposition Author(s): Beck, H., Schaefer, M., O'Donnell, J.P.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.200 (Depositor), 0.206 (DCC)
R-Value Work:
0.176 (Depositor), 0.181 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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.

Beck, H., Mesch, S., Zimmermann, S., Vakalopoulos, A., Lehmann, L., Gericke, K.M., Sussmeier, F., Baerfacker, L., Hillisch, A., Meier, K., Tersteegen, A., Buchmuller, A., Gerdes, C., Dietze-Torres, J., Kersten, E., Partikel, K., Brohl, A., Levilain, G., Heitmeier, S., Pfaff, N., Follmann, M.

(2025) J Med Chem 68: 12687-12707

PubMed: 40498640 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c00538
Primary Citation Related Structures:
9R8Q, 9R8R

PubMed Abstract:
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 ( t _1/2), resulting in a high controllability of the pharmacological action.

Organizational Affiliation

Bayer AG, Pharmaceuticals, Research & Development, 42113 Wuppertal, Germany.

Macromolecule Content

Total Structure Weight: 36.07 kDa
Atom Count: 2,666
Modeled Residue Count: 288
Deposited Residue Count: 299
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth L]	29	Homo sapiens	Mutation(s): 0 Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B [auth H]	259	Homo sapiens	Mutation(s): 0 Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin-2	C [auth I]	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JDJ (Subject of Investigation/LOI) Query on A1JDJ Download:Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate C₂₆ H₃₀ Cl N₅ O₇ S₂ UHRIYOJEACOYON-HKUYNNGSSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain J [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain J [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain J [auth H]	F [auth H], G [auth H], J [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain J [auth H] Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain J [auth H]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H SDF format, chain I [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H]	H, I [auth H], K [auth H], L [auth H]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H Focus chain I [auth H] Focus chain K [auth H] Focus chain L [auth H] Interactions & Density Focus chain H Focus chain I [auth H] Focus chain K [auth H] Focus chain L [auth H]