Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 206.79 kDa 
• Atom Count: 16091 
• Modelled Residue Count: 1696 
• Deposited Residue Count: 1704 
• Unique protein chains: 1

4DHL

Crystal structure of red kidney bean purple acid phosphatase in complex with Maybridge fragment MO07123

• PDB DOI: 10.2210/pdb4DHL/pdb

• Classification: HYDROLASE
• Organism(s): Phaseolus vulgaris
• Mutation(s): No 


• Deposited: 2012-01-29 Released: 2012-12-12 
• Deposition Author(s): Feder, D., Clayton, D.J., Hussein, W.M., Schenk, G., McGeary, R., Guddat, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Identification of purple acid phosphatase inhibitors by fragment-based screening: promising new leads for osteoporosis therapeutics.

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

(2012) Chem Biol Drug Des 80: 665-674

• PubMed: 22943065 
• DOI: 10.1111/cbdd.12001
• Primary Citation of Related Structures:  
  4DHL, 4DSY, 4DT2


• PubMed Abstract: 
  

Purple acid phosphatases are metalloenzymes found in animals, plants and fungi. They possess a binuclear metal centre to catalyse the hydrolysis of phosphate esters and anhydrides under acidic conditions. In humans, elevated purple acid phosphatases levels in sera are correlated with the progression of osteoporosis and metabolic bone malignancies, making this enzyme a target for the development of new chemotherapeutics to treat bone-related illnesses. To date, little progress has been achieved towards the design of specific and potent inhibitors of this enzyme that have drug-like properties. Here, we have undertaken a fragment-based screening approach using a 500-compound library identifying three inhibitors of purple acid phosphatases with K(i) values in the 30-60 μm range. Ligand efficiency values are 0.39-0.44 kcal/mol per heavy atom. X-ray crystal structures of these compounds in complex with a plant purple acid phosphatases (2.3-2.7 Å resolution) have been determined and show that all bind in the active site within contact of the binuclear centre. For one of these compounds, the phenyl ring is positioned within 3.5 Å of the binuclear centre. Docking simulations indicate that the three compounds fit into the active site of human purple acid phosphatases. These studies open the way to the design of more potent and selective inhibitors of purple acid phosphatases that can be tested as anti-osteoporotic drug leads.

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Organizational Affiliation: 

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purple acid phosphatase	A, B, D [auth C], C [auth D]	426	Phaseolus vulgaris	Mutation(s): 0  EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris) Explore P80366  Go to UniProtKB:  P80366

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, I, J, M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], JA [auth D], MA [auth D], SA [auth C], TA [auth C], U [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
0K7	DA [auth D], P [auth A], PA [auth C], X [auth B]	2-(4-methylphenyl)-1,3-thiazole-4-carboxylic acid C11 H9 N O2 S MTVWIZYQYPRZGZ-UHFFFAOYSA-N
SO4	FA [auth D], R [auth A], RA [auth C], S [auth A], Y [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	EA [auth D], Q [auth A], QA [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	BA [auth D], N [auth A], NA [auth C], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	GA [auth D], HA [auth D], IA [auth D], KA [auth D], LA [auth D], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	CA [auth D], O [auth A], OA [auth C], W [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0K7	Binding MOAD:  4DHL	Ki: 3.30e+4 (nM) from 1 assay(s)
	PDBBind:  4DHL	Ki: 3.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.097	α = 90
b = 126.097	β = 90
c = 297.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-29 
• Released Date: 2012-12-12 
Deposition Author(s): Feder, D., Clayton, D.J., Hussein, W.M., Schenk, G., McGeary, R., Guddat, L.W.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary