1FV9

Crystal structure of human microurokinase in complex with 2-amino-5-hydroxy-benzimidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Identification of novel inhibitors of urokinase via NMR-based screening.

Hajduk, P.J.Boyd, S.Nettesheim, D.Nienaber, V.Severin, J.Smith, R.Davidson, D.Rockway, T.Fesik, S.W.

(2000) J Med Chem 43: 3862-3866

  • DOI: 10.1021/jm0002228
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Using an NMR-based screen, a novel class of urokinase inhibitors were identified that contain a 2-aminobenzimidazole moiety. The inhibitory potency of this family of inhibitors is similar to that of inhibitors containing a guanidine or amidine group. ...

    Using an NMR-based screen, a novel class of urokinase inhibitors were identified that contain a 2-aminobenzimidazole moiety. The inhibitory potency of this family of inhibitors is similar to that of inhibitors containing a guanidine or amidine group. However, unlike previously described guanidino- or amidino-based inhibitors which have pK(a) values greater than 9.0, urokinase inhibitors containing a 2-aminobenzimidazole have pK(a) values of 7.5. Thus, 2-aminobenzimidazoles may have improved pharmacokinetic properties which could increase the bioavailability of inhibitors which contain this moiety. A crystal structure of one of the lead inhibitors, 2-amino-5-hydroxybenzimidazole, complexed with urokinase reveals the electrostatic and hydrophobic interactions that stabilize complex formation and suggests nearby subsites that may be accessed to increase the potency of this new series of urokinase inhibitors.


    Related Citations: 
    • Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite
      (2000) J Biol Chem 275: 7239

    Organizational Affiliation

    Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UROKINASE
A
245Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to UniProtKB:  P00749
NIH Common Fund Data Resources
PHAROS  P00749
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
172
Query on 172

Download CCD File 
A
2-AMINO-5-HYDROXY-BENZIMIDAZOLE
C7 H7 N3 O
FNSYWIPPPFVBAV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
172IC50 :  10000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.16α = 90
b = 53β = 90
c = 82.3γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2000-09-19 
  • Released Date: 2000-10-18 
  • Deposition Author(s): Nienaber, V.

Revision History 

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation