6SZP | pdb_00006szp

High resolution crystal structure of human DDAH-1 in complex with N-(4-Aminobutyl)-N'-(2-Methoxyethyl)guanidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M3BClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery ofN-(4-Aminobutyl)-N'-(2-methoxyethyl)guanidine as the First Selective, Nonamino Acid, Catalytic Site Inhibitor of Human Dimethylarginine Dimethylaminohydrolase-1 (hDDAH-1).

Lunk, I.Litty, F.A.Hennig, S.Vetter, I.R.Kotthaus, J.Altmann, K.S.Ott, G.Havemeyer, A.Carillo Garcia, C.Clement, B.Schade, D.

(2020) J Med Chem 63: 425-432

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01230
  • Primary Citation of Related Structures:  
    6SZP, 6SZQ

  • PubMed Abstract: 

    N -(4-Aminobutyl)- N '-(2-methoxyethyl)guanidine ( 8a ) is a potent inhibitor targeting the h DDAH-1 active site ( K i = 18 μM) and derived from a series of guanidine- and amidine-based inhibitors. Its nonamino acid nature leads to high selectivities toward other enzymes of the nitric oxide-modulating system. Crystallographic data of 8a -bound h DDAH-1 illuminated a unique binding mode. Together with its developed N -hydroxyguanidine prodrug 11 , 8a will serve as a most widely applicable, pharmacological tool to target DDAH-1-associated diseases.


  • Organizational Affiliation

    Department of Pharmaceutical and Medicinal Chemistry , Christian-Albrechts-University Kiel , Gutenbergstrasse 76 , D-24118 Kiel , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1297Homo sapiensMutation(s): 0 
Gene Names: DDAH1DDAH
EC: 3.5.3.18
UniProt & NIH Common Fund Data Resources
Find proteins for O94760 (Homo sapiens)
Explore O94760 
Go to UniProtKB:  O94760
PHAROS:  O94760
GTEx:  ENSG00000153904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94760
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.945α = 90
b = 54.945β = 90
c = 87.684γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M3BClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references