9PQ1 | pdb_00009pq1

The Discovery of a Novel Anticoagulant Mechanism: Factor XI Activation Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb9PQ1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-07-22 Released: 2026-07-29 
• Deposition Author(s): Hruza, A., Ogawa, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 
  0.298 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

The Discovery of a Novel Anticoagulant Mechanism: Factor XI Activation Inhibitors

Ellsworth, K., Nizner, P., Ogawa, A., Hruza, A., Wei, L., Yang, D., Lombardo, M., Sonatore, L., Barbieri, C.M., Wickham, A., Chamberlin, C., Nickbarg, E., Richards, M., Sauvegnat, B., Ziebell, M., Ho, T., Ali, A., Hicks, J., Sheth, P., Tata, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.09 kDa 
• Atom Count: 4,831 
• Modeled Residue Count: 602 
• Deposited Residue Count: 637 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	625	Homo sapiens	Mutation(s): 0  Gene Names: F11 EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens) Explore P03951  Go to UniProtKB:  P03951
GTEx:  ENSG00000088926
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P03951-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kininogen-1 light chain	B	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01042 (Homo sapiens) Explore P01042  Go to UniProtKB:  P01042
GTEx:  ENSG00000113889

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CJA	D [auth A]	{6-[(1,2,3-benzothiadiazol-5-yl)methoxy]-4-(piperidine-1-carbonyl)quinolin-2-yl}[4-(1H-pyrazol-1-yl)piperidin-1-yl]methanone C31 H31 N7 O3 S LYLBFDAAYFDIRY-UHFFFAOYSA-N
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free:  0.298 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.208	α = 90
b = 79.208	β = 90
c = 248.5	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-29 
Deposition Author(s): Hruza, A., Ogawa, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-07-29
  Type: Initial release