6OF5

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 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 10.1016/j.ejmech.2019.111611
  • Primary Citation of 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 ...

    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. Electronic address: r.mcgeary@uq.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fe(3+)-Zn(2+) purple acid phosphataseA,
B,
D [auth C],
C [auth D]
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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseE, H, K, M 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseF, I, J, N 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseG 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G43648DB
GlyCosmos:  G43648DB
GlyGen:  G43648DB
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseL 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80587NA
GlyCosmos:  G80587NA
GlyGen:  G80587NA
Small Molecules
Ligands 9 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CB [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MFJ Binding MOAD:  6OF5 Ki: 4500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • 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