6DXZ | pdb_00006dxz

Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) in complex with non-covalent benzothiazole-piperazine inhibitor ARN19702, in presence of Triton X-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.8 of the entry. See complete history

Literature

Molecular mechanism of activation of the immunoregulatory amidase NAAA.

Gorelik, A.Gebai, A.Illes, K.Piomelli, D.Nagar, B.

(2018) Proc Natl Acad Sci U S A 115: E10032-E10040

  • DOI: https://doi.org/10.1073/pnas.1811759115
  • Primary Citation Related Structures: 
    6DXW, 6DXX, 6DXY, 6DXZ, 6DY0, 6DY1, 6DY2, 6DY3

  • PubMed Abstract: 

    Palmitoylethanolamide is a bioactive lipid that strongly alleviates pain and inflammation in animal models and in humans. Its signaling activity is terminated through degradation by N -acylethanolamine acid amidase (NAAA), a cysteine hydrolase expressed at high levels in immune cells. Pharmacological inhibitors of NAAA activity exert profound analgesic and antiinflammatory effects in rodent models, pointing to this protein as a potential target for therapeutic drug discovery. To facilitate these efforts and to better understand the molecular mechanism of action of NAAA, we determined crystal structures of this enzyme in various activation states and in complex with several ligands, including both a covalent and a reversible inhibitor. Self-proteolysis exposes the otherwise buried active site of NAAA to allow catalysis. Formation of a stable substrate- or inhibitor-binding site appears to be conformationally coupled to the interaction of a pair of hydrophobic helices in the enzyme with lipid membranes, resulting in the creation of a linear hydrophobic cavity near the active site that accommodates the ligand's acyl chain.


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montreal, H3G0B1, Canada.

Macromolecule Content 

  • Total Structure Weight: 40.52 kDa 
  • Atom Count: 2,929 
  • Modeled Residue Count: 325 
  • Deposited Residue Count: 339 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-acylethanolamine acid amidase alpha-subunit107Oryctolagus cuniculusMutation(s): 0 
Gene Names: NAAA
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt
Find proteins for G1T7U7 (Oryctolagus cuniculus)
Explore G1T7U7 
Go to UniProtKB:  G1T7U7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T7U7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
N-acylethanolamine acid amidase beta-subunit232Oryctolagus cuniculusMutation(s): 0 
Gene Names: NAAA
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt
Find proteins for G1T7U7 (Oryctolagus cuniculus)
Explore G1T7U7 
Go to UniProtKB:  G1T7U7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T7U7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WTF

Query on WTF



Download:Ideal Coordinates CCD File
I [auth B][2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone
C21 H22 F N3 O3 S2
UKQOLPNYRVPCBM-AWEZNQCLSA-N
TRT

Query on TRT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
FRAGMENT OF TRITON X-100
C21 H36 O4
HEUDUECKTWTQQR-UHFFFAOYSA-N
TON

Query on TON



Download:Ideal Coordinates CCD File
J [auth B]2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL
C18 H30 O3
LBCZOTMMGHGTPH-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
27L

Query on 27L



Download:Ideal Coordinates CCD File
H [auth A]4-(2,4,4-trimethylpentan-2-yl)phenol
C14 H22 O
ISAVYTVYFVQUDY-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
WTF BindingDB:  6DXZ IC50: min: 228, max: 554 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.143α = 90
b = 159.143β = 90
c = 159.143γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.4: 2019-04-17
    Changes: Data collection, Structure summary
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.7: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2024-10-23
    Changes: Structure summary