6NMB

Tranexamic Acid is an Active Site Inhibitor of Urokinase Plasminogen Activator

• PDB DOI: https://doi.org/10.2210/pdb6NMB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-01-10 Released: 2019-03-06 
• Deposition Author(s): Law, R.H.P., Wu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.271 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Tranexamic acid is an active site inhibitor of urokinase plasminogen activator.

Wu, G., Mazzitelli, B.A., Quek, A.J., Veldman, M.J., Conroy, P.J., Caradoc-Davies, T.T., Ooms, L.M., Tuck, K.L., Schoenecker, J.G., Whisstock, J.C., Law, R.H.P.

(2019) Blood Adv 3: 729-733

• PubMed: 30814058 
• DOI: https://doi.org/10.1182/bloodadvances.2018025429
• Primary Citation of Related Structures:  
  6NMB


• PubMed Abstract: 
  

  TXA is an active-site inhibitor of uPA. TXA attenuates MDA-MB-231 BAG cell migration and inhibits endogenous uPA activity.

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Organizational Affiliation: 

ARC Centre of Excellence in Advanced Molecular Imaging, and.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 128.91 kDa 
• Atom Count: 8,028 
• Modelled Residue Count: 1,009 
• Deposited Residue Count: 1,124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A, B, C, D	281	Homo sapiens	Mutation(s): 0  Gene Names: PLAU EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens) Explore P00749  Go to UniProtKB:  P00749
PHAROS:  P00749 GTEx:  ENSG00000122861

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMH	F [auth A], H [auth B], J [auth C], L [auth D]	TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID C8 H15 N O2 GYDJEQRTZSCIOI-LJGSYFOKSA-N
NO3	E [auth A], G [auth B], I [auth C], K [auth D]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AMH	Binding MOAD:  6NMB	Ki: 2.01e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.271 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.043	α = 90
b = 65.446	β = 97.415
c = 111.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Currently 6NMB does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Law, R.H.P., Wu, G.

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-11-13
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description