7OV3

Crystal structure of pig purple acid phosphatase in complex with Maybridge fragment CC063346, dimethyl sulfoxide and citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach.

Feder, D.Mohd-Pahmi, S.H.Hussein, W.M.Guddat, L.W.McGeary, R.P.Schenk, G.

(2021) ChemMedChem 16: 3342-3359

  • DOI: https://doi.org/10.1002/cmdc.202100486
  • Primary Citation of Related Structures:  
    7OV2, 7OV3, 7OV8

  • PubMed Abstract: 

    Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the Maybridge TM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tartrate-resistant acid phosphatase type 5313Sus scrofaMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P09889 (Sus scrofa)
Explore P09889 
Go to UniProtKB:  P09889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09889
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
P [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT
Query on CIT

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R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
R2J (Subject of Investigation/LOI)
Query on R2J

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J [auth A],
K [auth A],
L [auth A]
N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine
C10 H13 N3
XDQYKASLVAVERE-UHFFFAOYSA-N
PGE
Query on PGE

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G [auth A],
H [auth A],
O [auth A],
Y [auth A],
Z [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

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Q [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)
Query on GOL

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W [auth A],
X [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS (Subject of Investigation/LOI)
Query on DMS

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AA [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
M [auth A],
N [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

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DA [auth A],
EA [auth A],
FA [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

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BA [auth A],
CA [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

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HA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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GA [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.085α = 90
b = 71.325β = 90
c = 77.553γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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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: 2022-01-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description