Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.70 kDa 
• Atom Count: 1941 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

1C5Q

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

• DOI: 10.2210/pdb1C5Q/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1999-12-22 Released: 2000-12-22 
• Deposition Author(s): Katz, B.A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P.A., Wang, J., Chan, H., Wong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator.

Katz, B.A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P.A., Wang, J., Chan, H., Wong, L.

(2000) Chem Biol 7: 299-312

• PubMed: 10779411 
• DOI: 10.1016/s1074-5521(00)00104-6
• Primary Citation of Related Structures:  
  1C5L, 1C5M, 1C5N, 1C5O, 1C5P, 1C5Q, 1C5R, 1C5S, 1C5T, 1C5U, 1C5V, 1C5W, 1C5X, 1C5Y, 1C5Z


• PubMed Abstract: 
  

Urokinase-type plasminogen activator (uPA) is a protease associated with tumor metastasis and invasion. Inhibitors of uPA may have potential as drugs for prostate, breast and other cancers. Therapeutically useful inhibitors must be selective for uPA and not appreciably inhibit the related, and structurally and functionally similar enzyme, tissue-type plasminogen activator (tPA), involved in the vital blood-clotting cascade.

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Organizational Affiliation: 

Axys Pharmaceutical Corporation, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRYPSIN)	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ESI (Subject of Investigation/LOI)	D [auth A]	4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE C9 H8 I N2 S YERQOXAYAFWFEJ-UHFFFAOYSA-O
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ESI	PDBBind:  1C5Q	Ki: 440 (nM) from 1 assay(s)
	Binding MOAD:  1C5Q	Ki: 440 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.87	α = 90
b = 64.11	β = 90
c = 69.49	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
X-PLOR	model building
Quanta	model building
Insight II	model building
X-PLOR	refinement
bioteX	data scaling
X-PLOR	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 1999-12-22 
• Released Date: 2000-12-22 
Deposition Author(s): Katz, B.A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P.A., Wang, J., Chan, H., Wong, L.

Revision History  

• Version 1.0: 2000-12-22
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description