7PWY | pdb_00007pwy

Structure of human dimeric ACMSD in complex with the inhibitor TES-1025


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural Basis of Human Dimeric alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase Inhibition With TES-1025.

Cianci, M.Giacche, N.Cialabrini, L.Carotti, A.Liscio, P.Rosatelli, E.De Franco, F.Gasparrini, M.Robertson, J.Amici, A.Raffaelli, N.Pellicciari, R.

(2022) Front Mol Biosci 9: 834700-834700

  • DOI: https://doi.org/10.3389/fmolb.2022.834700
  • Primary Citation of Related Structures:  
    7PWY

  • PubMed Abstract: 

    Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) stands at a branch point of the de novo NAD + synthesis pathway and plays an important role in maintaining NAD + homeostasis. It has been recently identified as a novel therapeutic target for a wide range of diseases, including inflammatory, metabolic disorders, and aging. So far, in absence of potent and selective enzyme inhibitors, only a crystal structure of the complex of human dimeric ACMSD with pseudo-substrate dipicolinic acid has been resolved. In this study, we report the crystal structure of the complex of human dimeric ACMSD with TES-1025, the first nanomolar inhibitor of this target, which shows a binding conformation different from the previously published predicted binding mode obtained by docking experiments. The inhibitor has a K i value of 0.85 ± 0.22 nM and binds in the catalytic site, interacting with the Zn 2+ metal ion and with residues belonging to both chains of the dimer. The results provide new structural information about the mechanism of inhibition exerted by a novel class of compounds on the ACMSD enzyme, a novel therapeutic target for liver and kidney diseases.


  • Organizational Affiliation

    Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
A, B, C, D
336Homo sapiensMutation(s): 0 
Gene Names: ACMSD
EC: 4.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDX5 (Homo sapiens)
Explore Q8TDX5 
Go to UniProtKB:  Q8TDX5
PHAROS:  Q8TDX5
GTEx:  ENSG00000153086 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDX5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8EK (Subject of Investigation/LOI)
Query on 8EK

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
2-[3-[(5-cyano-6-oxidanylidene-4-thiophen-2-yl-1H-pyrimidin-2-yl)sulfanylmethyl]phenyl]ethanoic acid
C18 H13 N3 O3 S2
RJQYGCGMQYVVIB-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
N [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
N [auth C],
P [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8EK BindingDB:  7PWY IC50: min: 10, max: 13 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.41α = 90
b = 92.579β = 90
c = 103.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 2.0: 2022-05-11
    Changes: Database references, Non-polymer description
  • Version 2.1: 2024-01-31
    Changes: Data collection, Refinement description