6SZP

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

• PDB DOI: https://doi.org/10.2210/pdb6SZP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-02 Released: 2019-12-25 
• Deposition Author(s): Hennig, S., Vetter, I.R., Schade, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

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

• PubMed: 31841335 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 32.94 kDa 
• Atom Count: 2,272 
• Modelled Residue Count: 275 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1	A	297	Homo sapiens	Mutation(s): 0  Gene Names: DDAH1, DDAH 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M3B (Subject of Investigation/LOI)	B [auth A]	(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine C8 H22 N4 O HBYRDDGQNQMGCZ-QMMMGPOBSA-N
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M3B	Binding MOAD:  6SZP	Ki: 1.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.230 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.945	α = 90
b = 54.945	β = 90
c = 87.684	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Hennig, S., Vetter, I.R., Schade, D.

Revision History  

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