1C5O

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: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.6 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

  • Primary Citation of Related Structures:  1C5L, 1C5M, 1C5N, 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 ...

    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 sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
259Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin
I
11Hirudo medicinalisN/A
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BAM
Query on BAM

Download SDF File 
Download CCD File 
H
BENZAMIDINE
C7 H9 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.460α = 90.00
b = 71.820β = 100.90
c = 72.850γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
bioteXdata collection
Insight IImodel building
bioteXdata scaling
X-PLORmodel building
bioteXdata reduction
Quantamodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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