6NMB | pdb_00006nmb

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.271 (Depositor), 0.245 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1182/bloodadvances.2018025429
Primary Citation 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.

Organizational Affiliation

ARC Centre of Excellence in Advanced Molecular Imaging, and.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMH Query on AMH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	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		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.271 (Depositor), 0.245 (DCC)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.223 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

Law, R.H.P.

Wu, G.

Revision History (Full details and data files)

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
Version 1.4: 2024-10-30
Changes: Structure summary