6SZP

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 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.9b01230
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>N </i>-(4-aminobutyl)- <i>N' </i>-(2-methoxyethyl)guanidine ( <b>8a </b>) is as a potent inhibitor targeting the <b>h </b>DDAH-1 active site (K <sub>i </sub> = 18 µM) and derived from a series of guanidine- and amidine-based inhibitors. Its non- ...

    N -(4-aminobutyl)- N' -(2-methoxyethyl)guanidine ( 8a ) is as 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 non-amino acid nature leads to high selectivities towards 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, currently available pharmacological tool to target DDAH-1-associated diseases.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
A
297Homo sapiensMutation(s): 0 
Gene Names: DDAH1 (DDAH)
EC: 3.5.3.18
Find proteins for O94760 (Homo sapiens)
Go to Gene View: DDAH1
Go to UniProtKB:  O94760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
M3B
Query on M3B

Download SDF File 
Download CCD File 
A
(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine
C8 H22 N4 O
HBYRDDGQNQMGCZ-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 54.945α = 90.00
b = 54.945β = 90.00
c = 87.684γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references