8GSQ | pdb_00008gsq

Structure based studies reveal an atypical antipsychotic drug candidate - Paliperidone as a potent hSOD1 modulator with implications in ALS treatment.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-based discovery of an antipsychotic drug, paliperidone, as a modulator of human superoxide dismutase 1: a potential therapeutic target in amyotrophic lateral sclerosis.

Aouti, S.Padavattan, S.Padmanabhan, B.

(2023) Acta Crystallogr D Struct Biol 79: 531-544

  • DOI: https://doi.org/10.1107/S2059798323003649
  • Primary Citation Related Structures: 
    8GSQ

  • PubMed Abstract: 

    Aggregates of the antioxidant superoxide dismutase 1 (SOD1) are one of the major contributors to the pathogenesis of amyotrophic lateral sclerosis (ALS). Mutations in SOD1 lead to an unstable structure and aggregation that perturbs the balance of reactive oxygen species in cells. Oxidation damage to the solvent-exposed Trp32 also causes aggregation of SOD1. Here, the FDA-approved antipsychotic drug paliperidone is identified to interact with Trp32 of SOD1 by structure-based pharmacophore mapping and crystallographic studies. Paliperidone is used for the treatment of schizophrenia. The crystal structure of the complex with SOD1, refined to 2.1 Å resolution, revealed that the ligand binds to the SOD1 β-barrel in the β-strand 2 and 3 regions, which are known to scaffold SOD1 fibrillation. The drug also makes substantial π-π interaction with Trp32. Microscale thermophoresis studies confirm significant binding affinity of the compound, suggesting that the ligand can inhibit or prevent tryptophan oxidation. Thus, the antipsychotic drug paliperidone or a derivative may avert SOD1 aggregation and can be used as a lead for ALS drug development.


  • Organizational Affiliation
    • Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka 560029, India.

Macromolecule Content 

  • Total Structure Weight: 160.8 kDa 
  • Atom Count: 12,072 
  • Modeled Residue Count: 1,519 
  • Deposited Residue Count: 1,540 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, D, F, I
A, B, D, F, I, J
154Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]155Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
E, G
154Homo sapiensMutation(s): 0 
Gene Names: HEL-S-44
EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]153Homo sapiensMutation(s): 0 
Gene Names: HEL-S-44
EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K4I
(Subject of Investigation/LOI)

Query on K4I



Download:Ideal Coordinates CCD File
X [auth H](9~{R})-3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-9-oxidanyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
C23 H27 F N4 O3
PMXMIIMHBWHSKN-LJQANCHMSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth A]
N [auth B]
P [auth C]
R [auth D]
T [auth E]
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
S [auth E]
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth H],
Y [auth I],
Z [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.793α = 90
b = 202.455β = 90
c = 143.996γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Indian Council of Medical ResearchIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-11-13
    Changes: Structure summary