1C5N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.8 of the entry. See complete history


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

  • DOI: 10.1016/s1074-5521(00)00104-6
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Organizational Affiliation

    Axys Pharmaceutical Corporation, South San Francisco, CA 94080, USA. brad_katz@axyspharm.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin
I
10Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ESI
Query on ESI

Download CCD File 
H
4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE
C9 H8 I N2 S
YERQOXAYAFWFEJ-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
IL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESIKi :  20000   nM  PDBBind
ESIKi:  20000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.14α = 90
b = 72.26β = 101.23
c = 73.09γ = 90
Software Package:
Software NamePurpose
bioteXdata collection
bioteXdata reduction
X-PLORmodel building
Quantamodel building
Insight IImodel building
X-PLORrefinement
bioteXdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2011-08-03
    Changes: Atomic model
  • Version 1.4: 2011-08-17
    Changes: Database references
  • Version 1.5: 2012-12-12
    Changes: Other
  • Version 1.6: 2013-03-13
    Changes: Other
  • Version 1.7: 2016-06-01
    Changes: Source and taxonomy
  • Version 1.8: 2017-10-04
    Changes: Advisory, Refinement description