2JEW

Crystal structure of ((2S)-5-amino-2-((1-n-propyl-1H-imidazol-4-yl) methyl)pentanoic acid) UK396,082 a TAFIa inhibitor, Bound to Activated Porcine Pancreatic carboxypeptidaseB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Discovery of potent & selective inhibitors of activated thrombin-activatable fibrinolysis inhibitor for the treatment of thrombosis.

Bunnage, M.E.Blagg, J.Steele, J.Owen, D.R.Allerton, C.McElroy, A.B.Miller, D.Ringer, T.Butcher, K.Beaumont, K.Evans, K.Gray, A.J.Holland, S.J.Feeder, N.Moore, R.S.Brown, D.G.

(2007) J Med Chem 50: 6095-6103

  • DOI: https://doi.org/10.1021/jm0702433
  • Primary Citation of Related Structures:  
    2JEW

  • PubMed Abstract: 

    Thrombin-activatable fibrinolysis inhibitor (TAFI) has emerged as a key link between the coagulation and fibrinolysis cascades and represents a promising new target for the treatment of thrombosis. A novel series of imidazolepropionic acids has been designed that exhibit high potency against activated TAFI (TAFIa) and excellent selectivity over plasma carboxypeptidase N (CPN). Structure activity relationships suggest that the imidazole moiety plays a key role in binding to the catalytic zinc of TAFIa, and this has been supported by crystallographic studies using porcine pancreatic carboxypeptidase B as a surrogate for TAFIa. The SAR program led to the identification of 21 (TAFIa Ki = 10 nM, selectivity TAFIa/CPN > 1000) as a candidate for clinical development. Compound 21 exhibited antithrombotic efficacy in a rabbit model of venous thrombosis, yet had no effect on surgical bleeding in the rabbit. In addition, 21 exhibited an excellent preclinical and clinical pharmacokinetic profile, characterized by paracellular absorption, low clearance, and a low volume of distribution, fully consistent with its physicochemical properties of low molecular weight (MW = 239) and high hydrophilicity (log D = -2.8). These data indicate 21 (UK-396,082) has potential as a novel TAFIa inhibitor for the treatment of thrombosis and other fibrin-dependent diseases in humans.


  • Organizational Affiliation

    Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Kent, U.K. mark.bunnage@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE B306Sus scrofaMutation(s): 0 
EC: 3.4.17.2
UniProt
Find proteins for P09955 (Sus scrofa)
Explore P09955 
Go to UniProtKB:  P09955
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09955
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
720
Query on 720

Download Ideal Coordinates CCD File 
D [auth A](2S)-5-AMINO-2-[(1-PROPYL-1H-IMIDAZOL-4-YL)METHYL]PENTANOIC ACID
C12 H21 N3 O2
OTDGPKRCQXSTPV-JTQLQIEISA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
720 Binding MOAD:  2JEW Ki: 206 (nM) from 1 assay(s)
PDBBind:  2JEW Ki: 206 (nM) from 1 assay(s)
BindingDB:  2JEW Ki: 206 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.09α = 90
b = 84.09β = 90
c = 92.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-20
    Changes: Data collection, Database references
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description