8PC4

MEMBRANE TARGET COMPLEX 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.301 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PEClick on this verticalbar to view detailsBest fitted DXCClick on this verticalbar to view detailsBest fitted HCZClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

NAPE-PLD is target of thiazide diuretics.

Chiarugi, S.Margheriti, F.De Lorenzi, V.Martino, E.Margheritis, E.G.Moscardini, A.Marotta, R.Chaves-Sanjuan, A.Del Seppia, C.Federighi, G.Lapi, D.Bandiera, T.Rapposelli, S.Scuri, R.Bolognesi, M.Garau, G.

(2025) Cell Chem Biol 

  • DOI: https://doi.org/10.1016/j.chembiol.2025.01.008
  • Primary Citation of Related Structures:  
    8P90, 8P96, 8PC4

  • PubMed Abstract: 

    Thiazide and thiazide-like diuretics are among the most efficacious and used drugs for the treatment of hypertension, edema, and major cardiovascular outcomes. Despite more then than six decades of clinical use, the molecular target and mechanism of action by which these drugs cure hypertension after long-term use have remained mysterious. Here we report the discovery and validation of a previously unknown renal and extrarenal target of these antihypertensives, the membrane-associated phospholipase N-acylphosphatidylethanolamine-specific phospholipase D (NAPE-PLD) of the endocannabinoid system. Structural and functional insights, together with preclinical studies in hypertensive rats, disclose the molecular and physiological basis by which thiazides cause acute diuresis and, at the same time, the distinctive chronic reduction of vascular resistance. Our results shed light on the mechanism of treatment of hypertension and will be useful for developing more efficacious medications for the management of vascular risk factors, as well as associated leukoencephalopathies and myelin disorders.


  • Organizational Affiliation

    BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Piazza San Silvestro 12, 56127 Pisa, Italy; Laboratorio NEST, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
A, B
393Homo sapiensMutation(s): 0 
Gene Names: NAPEPLDC7orf18
EC: 3.1.4.54
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IQ20 (Homo sapiens)
Explore Q6IQ20 
Go to UniProtKB:  Q6IQ20
PHAROS:  Q6IQ20
GTEx:  ENSG00000161048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IQ20
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE (Subject of Investigation/LOI)
Query on 3PE

Download Ideal Coordinates CCD File 
E [auth A],
P [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
DXC (Subject of Investigation/LOI)
Query on DXC

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
HCZ (Subject of Investigation/LOI)
Query on HCZ

Download Ideal Coordinates CCD File 
S [auth B]6-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide 1,1-dioxide
C7 H8 Cl N3 O4 S2
JZUFKLXOESDKRF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.301 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.389α = 90
b = 94.389β = 90
c = 442.325γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PEClick on this verticalbar to view detailsBest fitted DXCClick on this verticalbar to view detailsBest fitted HCZClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-26 
  • Deposition Author(s): Garau, G.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references, Structure summary
  • Version 1.2: 2025-03-12
    Changes: Database references