6OF5 | pdb_00006of5

The crystal structure of dodecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OF5

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis.

Feder, D.Kan, M.W.Hussein, W.M.Guddat, L.W.Schenk, G.McGeary, R.P.

(2019) Eur J Med Chem 182: 111611-111611

  • DOI: https://doi.org/10.1016/j.ejmech.2019.111611
  • Primary Citation Related Structures: 
    6OF5, 6OFD

  • PubMed Abstract: 

    Purple acid phosphatases (PAPs) are binuclear hydrolases that catalyze the hydrolysis of phosphorylated substrates under acidic to neutral conditions. Elevated serum concentrations of PAP are observed in patients suffering from osteoporosis, identifying this enzyme as a potential target for the development of novel therapeutic agents to treat this disease. α-Alkoxy-substituted naphthylmethylphosphonic acid derivatives have been identified previously as molecules that bind with high affinity to PAPs, and docking studies suggest that longer alkyl chains may increase the binding affinities of such compounds. Here, we synthesized several derivatives and tested their inhibitory effect against pig and red kidney bean PAPs. The most potent inhibitor within this series is the octadecyl derivative, which has a K i value of ∼200 nM. Crystal structures of the dodecyl and octadecyl derivatives bound to red kidney bean PAP show that the length of the alkyl chain influences the ability of the phosphonate group to interact directly with the bimetallic center. These structures represent the first examples of potent inhibitors bound to a PAP that have drug-like properties. This study provides a starting point for the development of much needed new treatments for osteoporosis.


  • Organizational Affiliation
    • The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, QLD, 4072, Australia.

Macromolecule Content 

  • Total Structure Weight: 210.94 kDa 
  • Atom Count: 15,939 
  • Modeled Residue Count: 1,695 
  • Deposited Residue Count: 1,704 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(3+)-Zn(2+) purple acid phosphataseA,
B,
C [auth D],
D [auth C]
426Phaseolus vulgarisMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris)
Explore P80366 
Go to UniProtKB:  P80366
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80366
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, H, K, M
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G11971MR
GlyCosmos: G11971MR
GlyGen: G11971MR
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, I, J, N
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G18638YB
GlyCosmos: G18638YB
GlyGen: G18638YB
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
G
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G43648DB
GlyCosmos: G43648DB
GlyGen: G43648DB
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
L
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G80587NA
GlyCosmos: G80587NA
GlyGen: G80587NA

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MFJ
(Subject of Investigation/LOI)

Query on MFJ



Download:Ideal Coordinates CCD File
CA [auth A][(R)-{[(2E,4Z,8Z)-dodeca-2,4,8-trien-1-yl]oxy}(naphthalen-1-yl)methyl]phosphonic acid
C23 H29 O4 P
NQBCLJOVYMZXNE-MNTXUOLASA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
FA [auth B]
IB [auth C]
JB [auth C]
Q [auth A]
SA [auth D]
FA [auth B],
IB [auth C],
JB [auth C],
Q [auth A],
SA [auth D],
UA [auth D],
VB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
DB [auth D],
EB [auth D],
FB [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
KB [auth C],
LA [auth B],
LB [auth C],
MA [auth B],
MB [auth C],
NA [auth B],
NB [auth C],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
VA [auth D],
WA [auth D],
XA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CB [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
DA [auth B],
GB [auth C],
O [auth A],
QA [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AB [auth D]
BB [auth D]
OA [auth B]
PA [auth B]
QB [auth C]
AB [auth D],
BB [auth D],
OA [auth B],
PA [auth B],
QB [auth C],
RB [auth C],
SB [auth C],
TA [auth D],
TB [auth C],
UB [auth C],
X [auth A],
Y [auth A],
Z [auth A],
ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
EA [auth B],
HB [auth C],
P [auth A],
RA [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
OB [auth C],
PB [auth C],
V [auth A],
W [auth A],
YA [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.808α = 90
b = 126.808β = 90
c = 298.211γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP0986292
Australian Research Council (ARC)Australia150104358

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary