Crystal structure of dimethylarginine dimethylaminohydrolase-1 (DDAH-1) in complex with N5-(1-iminopropyl)-L-ornithine

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Developing dual and specific inhibitors of dimethylarginine dimethylaminohydrolase-1 and nitric oxide synthase: toward a targeted polypharmacology to control nitric oxide.

Wang, Y.Monzingo, A.F.Hu, S.Schaller, T.H.Robertus, J.D.Fast, W.

(2009) Biochemistry 48: 8624-8635

  • DOI: https://doi.org/10.1021/bi9007098
  • Primary Citation of Related Structures:  
    3I2E, 3I4A

  • PubMed Abstract: 

    Molecules that block nitric oxide's (NO) biosynthesis are of significant interest. For example, nitric oxide synthase (NOS) inhibitors have been suggested as antitumor therapeutics, as have inhibitors of dimethylarginine dimethylaminohydrolase (DDAH), an enzyme that catabolizes endogenous NOS inhibitors. Dual-targeted inhibitors hold promise as more effective reagents to block NO biosynthesis than single-targeted compounds. In this study, a small set of known NOS inhibitors are surveyed as inhibitors of recombinant human DDAH-1. From these, an alkylamidine scaffold is selected for homologation. Stepwise lengthening of one substituent converts an NOS-selective inhibitor into a dual-targeted NOS/DDAH-1 inhibitor and then into a DDAH-1 selective inhibitor, as seen in the inhibition constants of N5-(1-iminoethyl)-, N5-(1-iminopropyl)-, N5-(1-iminopentyl)- and N(5)-(1-iminohexyl)-l-ornithine for neuronal NOS (1.7, 3, 20, >1,900 microM, respectively) and DDAH-1 (990, 52, 7.5, 110 microM, respectively). A 1.9 A X-ray crystal structure of the N5-(1-iminopropyl)-L-ornithine:DDAH-1 complex indicates covalent bond formation between the inhibitor's amidino carbon and the active-site Cys274, and solution studies show reversible competitive inhibition, consistent with a reversible covalent mode of DDAH inhibition by alkylamidine inhibitors. These represent a versatile scaffold for the development of a targeted polypharmacological approach to control NO biosynthesis.

  • Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
A, B
308Homo sapiensMutation(s): 0 
Gene Names: DDAHDDAH1
UniProt & NIH Common Fund Data Resources
Find proteins for O94760 (Homo sapiens)
Explore O94760 
Go to UniProtKB:  O94760
GTEx:  ENSG00000153904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94760
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LN5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C8 H17 N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
LN5 BindingDB:  3I4A Ki: min: 5.20e+4, max: 1.45e+5 (nM) from 2 assay(s)
IC50: 3.00e+5 (nM) from 1 assay(s)
PDBBind:  3I4A Ki: 5.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.6α = 90
b = 80.13β = 90.13
c = 73.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-07-16
    Changes: Other
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description