8BRN | pdb_00008brn

Crystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of an alpha-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches.

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

(2023) Eur J Med Chem 254: 115383-115383

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115383
  • Primary Citation Related Structures: 
    8BRN

  • PubMed Abstract: 

    Purple acid phosphatases (PAPs) are ubiquitous binuclear metallohydrolases that have been isolated from various animals, plants and some types of fungi. In humans and mice, elevated PAP activity in osteoclasts is associated with osteoporosis, making human PAP an attractive target for the development of anti-osteoporotic drugs. Based on previous studies focusing on phosphonate scaffolds, as well as a new crystal structure of a PAP in complex with a derivative of a previously synthesized α-aminonaphthylmethylphosphonic acid, phosphonates 24-40 were designed as new PAP inhibitor candidates. Subsequent docking studies predicted that all of these compounds are likely to interact strongly with the active site of human PAP and most are likely to interact strongly with the active site of pig PAP. The seventeen candidates were synthesized with good yields and nine of them (26-28, 30, 33-36 and 38) inhibit in the sub-micromolar to nanomolar range against pig PAP, with 28 and 35 being the most potent mammalian PAP inhibitors reported with K i values of 168 nM and 186 nM, respectively. This study thus paves the way for the next stage of drug development for phosphonate inhibitors of PAPs as anti-osteoporotic agents.


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

Macromolecule Content 

  • Total Structure Weight: 226.08 kDa 
  • Atom Count: 18,800 
  • Modeled Residue Count: 1,707 
  • Deposited Residue Count: 1,712 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(3+)-Zn(2+) purple acid phosphatase
A, B, C, D
428Phaseolus 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: 6
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, K, Q
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-[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
F
6N-Glycosylation
Entity ID: 4
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
G,
I,
N,
P,
S,
G,
I,
N,
P,
S,
U [auth V]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G18638YB
GlyCosmos: G18638YB
GlyGen: G18638YB
Entity ID: 5
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
H, J
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G43648DB
GlyCosmos: G43648DB
GlyGen: G43648DB
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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
L
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G17538MY
GlyCosmos: G17538MY
GlyGen: G17538MY
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G79924RM
GlyCosmos: G79924RM
GlyGen: G79924RM
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
R
4N/AN-Glycosylation
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
T
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G80587NA
GlyCosmos: G80587NA
GlyGen: G80587NA

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R9X
(Subject of Investigation/LOI)

Query on R9X



Download:Ideal Coordinates CCD File
AB [auth A],
FC [auth B],
LD [auth C],
MD [auth C],
VE [auth D]
[(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid
C21 H30 N O4 P
QQNUSDSQHYRTKZ-OAQYLSRUSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A],
CE [auth D],
KC [auth C],
SD [auth D],
VC [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
DB [auth B]
FB [auth B]
GB [auth B]
GC [auth C]
GD [auth C]
DB [auth B],
FB [auth B],
GB [auth B],
GC [auth C],
GD [auth C],
HB [auth B],
HC [auth C],
HD [auth C],
IC [auth C],
PD [auth D],
X [auth A],
YA [auth A],
Z [auth A]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PGE

Query on PGE



Download:Ideal Coordinates CCD File
BA [auth A]
EB [auth B]
IB [auth B]
JC [auth C]
QD [auth D]
BA [auth A],
EB [auth B],
IB [auth B],
JC [auth C],
QD [auth D],
Y [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AE [auth D]
BE [auth D]
CA [auth A]
DA [auth A]
EA [auth A]
AE [auth D],
BE [auth D],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
JB [auth B],
KB [auth B],
LB [auth B],
MB [auth B],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
QB [auth B],
QC [auth C],
RB [auth B],
RC [auth C],
SC [auth C],
TC [auth C],
TD [auth D],
UC [auth C],
UD [auth D],
VD [auth D],
WD [auth D],
XD [auth D],
YD [auth D],
ZD [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AC [auth B]
AD [auth C]
BC [auth B]
BD [auth C]
CC [auth B]
AC [auth B],
AD [auth C],
BC [auth B],
BD [auth C],
CC [auth B],
CD [auth C],
DD [auth C],
ED [auth C],
EE [auth D],
FE [auth D],
GE [auth D],
HE [auth D],
ID [auth C],
IE [auth D],
JA [auth A],
JD [auth C],
JE [auth D],
KA [auth A],
KD [auth C],
KE [auth D],
LA [auth A],
LE [auth D],
MA [auth A],
ME [auth D],
NA [auth A],
NE [auth D],
OA [auth A],
OE [auth D],
PA [auth A],
PE [auth D],
QA [auth A],
RA [auth A],
SA [auth A],
SE [auth D],
TA [auth A],
TB [auth B],
TE [auth D],
UA [auth A],
UB [auth B],
UE [auth D],
VA [auth A],
VB [auth B],
WB [auth B],
XB [auth B],
XC [auth C],
YB [auth B],
YC [auth C],
ZA [auth A],
ZB [auth B],
ZC [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
RD [auth D]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BB [auth B],
LC [auth C],
ND [auth D],
V [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
DE [auth D],
IA [auth A],
SB [auth B],
WC [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
CB [auth B],
MC [auth C],
OD [auth D],
W [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DC [auth B]
FD [auth C]
QE [auth D]
RE [auth D]
WA [auth A]
DC [auth B],
FD [auth C],
QE [auth D],
RE [auth D],
WA [auth A],
XA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
EC [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.859α = 90
b = 125.859β = 90
c = 298.339γ = 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)AustraliaDP150104358

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary