5LYI

Crystal structure of 1 in complex with tafCPB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Sulfamide as Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).

Halland, N., Czech, J., Czechtizky, W., Evers, A., Follmann, M., Kohlmann, M., Schreuder, H.A., Kallus, C.

(2016) J Med Chem 59: 9567-9573

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01276
  • Primary Citation of Related Structures:  
    5LYD, 5LYF, 5LYI, 5LYL

  • PubMed Abstract: 

    Previously disclosed TAFIa inhibitors having a urea zinc-binding motif were used as the starting point for the development of a novel class of highly potent inhibitors having a sulfamide zinc-binding motif. High-resolution X-ray cocrystal structures were used to optimize the structures and reveal a highly unusual sulfamide configuration. A selected sulfamide was profiled in vitro and in vivo and displayed a promising ADMET profile.

    • Organizational Affiliation: 

    Sanofi R&D , Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase B307Sus scrofaMutation(s): 0 
Gene Names: CPB1, CPB
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T4F
Query on T4F
Download Ideal Coordinates CCD File 
E [auth A](2~{S})-6-azanyl-2-[[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(1~{R},2~{S},4~{R})-1,7,7-trimethyl-2-bicyclo[2.2.1]hepta nyl]amino]propan-2-yl]sulfamoylamino]hexanoic acid
C25 H46 N4 O5 S
IQHARPQKKWCGEY-PHGOAHNDSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.039α = 90
b = 82.039β = 90
c = 95.813γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references