Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23702.96 
• Atom Count: 1697 
• 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


• 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 

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 
• Primary Citation of Related Structures:  
  1C5Z, 1C5Y, 1C5X, 1C5W, 1C5V, 1C5U, 1C5T, 1C5S, 1C5R, 1C5P, 1C5O, 1C5N, 1C5M, 1C5L


• 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

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ESI	Ki: 440 nM (100) BINDINGDB
ESI	Ki: 440 nM BINDINGMOAD
ESI	Ki: 440 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 63.870	α = 90.00
b = 64.110	β = 90.00
c = 69.490	γ = 90.00

Software Package:

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

Structure Validation

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-04
  Type: Advisory, Refinement description