4H42

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

• PDB DOI: https://doi.org/10.2210/pdb4H42/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2012-09-14 Released: 2013-10-30 
• Deposition Author(s): Yu, H.-Y., Gao, D., Zhang, X., Jiang, L.-G., Hong, Z.-B., Yuan, C., Fang, X., Wang, J.-D., Huang, M.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.285 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Literature

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

Yu, H.-Y., Gao, D., Xu, Z., Jiang, L.-G., Hong, Z.-B., Fan, X., Yuan, C., Wang, J.-D., Huang, M.

(2013) Chin J Struct Chem 32: 961-968

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 28.49 kDa 
• Atom Count: 2,111 
• Modelled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	248	Homo sapiens	Mutation(s): 2  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
PG6	C [auth U]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
11E	B [auth U]	N-[(2-amino-1,3-benzothiazol-6-yl)carbonyl]glycine C10 H9 N3 O3 S JTXHRLUPQXMVPR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
11E	PDBBind:  4H42	Ki: 3.41e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.285 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.916	α = 90
b = 120.916	β = 90
c = 42.875	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Yu, H.-Y., Gao, D., Zhang, X., Jiang, L.-G., Hong, Z.-B., Yuan, C., Fang, X., Wang, J.-D., Huang, M.-D.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references, Derived calculations