3TK5

Factor Xa in complex with D102-4380

• PDB DOI: https://doi.org/10.2210/pdb3TK5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-08-25 Released: 2012-08-29 
• Deposition Author(s): Suzuki, M., Mochizuki, A., Nagata, T., Takano, H., Kanno, H., Kishida, M., Ohta, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Zwitter ionic potent durable orally active Factor Xa inhibitor.

Mochizuki, A., Nagata, T., Takano, H., Kanno, H., Kishida, M., Suzuki, M., Ohta, T.

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: 32.8 kDa 
• Atom Count: 2,429 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor X heavy chain	A	233	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor X light chain	B	54	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D1Q	E [auth A]	4-{3-[(4-chlorophenyl)amino]-3-oxopropyl}-3-({[5-(propan-2-yl)-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridin-2-yl]carbonyl}amino)benzoic acid C26 H27 Cl N4 O4 S FQNIFNHOEQFSHE-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D1Q	BindingDB:  3TK5	IC50: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.278	α = 90
b = 71.928	β = 90
c = 78.775	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Suzuki, M., Mochizuki, A., Nagata, T., Takano, H., Kanno, H., Kishida, M., Ohta, T.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary