1C5X

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

• PDB DOI:  https://doi.org/10.2210/pdb1C5X/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• 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: 1.75 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

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: https://doi.org/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]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 32.01 kDa 
• Atom Count: 2,534 
• Modelled Residue Count: 257 
• Deposited Residue Count: 276 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UROKINASE-TYPE PLASMINOGEN ACTIVATOR)	A	23	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UROKINASE-TYPE PLASMINOGEN ACTIVATOR)	B	253	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ESI	F [auth B]	4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE C9 H8 I N2 S YERQOXAYAFWFEJ-UHFFFAOYSA-O
FLC	C [auth B], D [auth B], E [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
ESI	Binding MOAD:  1C5X	Ki: 210 (nM) from 1 assay(s)
	PDBBind:  1C5X	Ki: 210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.09	α = 90
b = 49.78	β = 113.29
c = 66.65	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

Entry History 

Deposition Data

• 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