6DXX

Human 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: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylethanolamine-hydrolyzing acid amidase subunit alpha
A, C, E
107Homo sapiensMutation(s): 0 
Gene Names: NAAAASAHLPLT
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02083 (Homo sapiens)
Explore Q02083 
Go to UniProtKB:  Q02083
PHAROS:  Q02083
GTEx:  ENSG00000138744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02083
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q02083-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylethanolamine-hydrolyzing acid amidase subunit beta
B, D, F
234Homo sapiensMutation(s): 0 
Gene Names: NAAAASAHLPLT
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02083 (Homo sapiens)
Explore Q02083 
Go to UniProtKB:  Q02083
PHAROS:  Q02083
GTEx:  ENSG00000138744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02083
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q02083-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WTF
Query on WTF

Download Ideal Coordinates CCD File 
BA [auth D],
JA [auth F],
N [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
TON
Query on TON

Download Ideal Coordinates CCD File 
EA [auth E],
J [auth A],
T [auth C]
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 
CA [auth E],
H [auth A],
K [auth B],
O [auth C],
U [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
AA [auth D]
GA [auth F]
HA [auth F]
IA [auth F]
S [auth C]
AA [auth D],
GA [auth F],
HA [auth F],
IA [auth F],
S [auth C],
Z [auth D]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth E]
FA [auth F]
I [auth A]
L [auth B]
M [auth B]
DA [auth E],
FA [auth F],
I [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
R [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
WTF BindingDB:  6DXX IC50: min: 158, max: 554 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.61α = 90
b = 99.798β = 96.13
c = 92.756γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary