1O5G

Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA).

Katz, B.A.Luong, C.Ho, J.D.Somoza, J.R.Gjerstad, E.Tang, J.Williams, S.R.Verner, E.Mackman, R.L.Young, W.B.Sprengeler, P.A.Chan, H.Mortara, K.Janc, J.W.McGrath, M.E.

(2004) J Mol Biol 344: 527-547

  • DOI: 10.1016/j.jmb.2004.09.032
  • Primary Citation of Related Structures:  
    1O5G, 1O5F, 1O5E, 1O5D, 1O5C, 1O5B, 1O5A

  • PubMed Abstract: 
  • A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences pres ...

    A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences present in comparisons of natural proteases. Crystallography and enzymology involving WT and Ala190 uPA were used to calculate free energy binding contributions of hydrogen bonds involving the Ser190 hydroxyl group (O(gamma)(Ser190)) responsible for the remarkable selectivity of 6-halo-5-amidinoindole and 6-halo-5-amidinobenzimidazole inhibitors toward uPA and against natural Ala190 protease anti-targets. Crystal structures of uPA complexes of novel, active site-directed arylguanidine and 2-aminobenzimidazole inhibitors of WT uPA, together with associated K(i) values for WT and Ala190 uPA, also indicate a significant role of Ser190 in the binding of these classes of uPA inhibitors. Structures and associated K(i) values for a lead inhibitor (CA-11) bound to uPA and to five other proteases, as well as for other leads bound to multiple proteases, help reveal the features responsible for the potency (K(i)=11nM) and selectivity of the remarkably small inhibitor, CA-11. The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets.


    Organizational Affiliation

    Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. brad.katz@celera.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinL36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinH259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hirudin IIIB'I11Hirudo medicinalisMutation(s): 1 
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CR9
Query on CR9

Download CCD File 
H
2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL-2-YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE
C21 H23 F N4 O2
CMCDWLMEDRBWIR-GTNSWQLSSA-N
 Ligand Interaction
CA
Query on CA

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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 %)
CR9Ki:  11000   nM  BindingDB
CR9Ki:  11000   nM  Binding MOAD
CR9Ki :  11000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.34α = 90
b = 72.04β = 100.83
c = 72.95γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
X-PLORrefinement
CrystalCleardata scaling
Quantamodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    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: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-03-13
    Changes: Other