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- PDB-7kh8: Human LMPTP in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7kh8
TitleHuman LMPTP in complex with inhibitor
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein Tyrosine Phosphatase / LMWPTP / Inhibitor / Complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / : / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family
Similarity search - Domain/homology
NITRATE ION / Chem-WE7 / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsStanford, S.M. / Diaz, M.A. / Ardecky, R.J. / Zou, J. / Roosild, T. / Holmes, Z.J. / Hedrick, M.P. / Rodiles, S. / Santelli, E. / Chung, T.D.Y. ...Stanford, S.M. / Diaz, M.A. / Ardecky, R.J. / Zou, J. / Roosild, T. / Holmes, Z.J. / Hedrick, M.P. / Rodiles, S. / Santelli, E. / Chung, T.D.Y. / Jackson, M.R. / Bottini, N. / Pinkerton, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK106233 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Orally Bioavailable Purine-Based Inhibitors of the Low-Molecular-Weight Protein Tyrosine Phosphatase.
Authors: Stanford, S.M. / Diaz, M.A. / Ardecky, R.J. / Zou, J. / Roosild, T. / Holmes, Z.J. / Nguyen, T.P. / Hedrick, M.P. / Rodiles, S. / Guan, A. / Grotegut, S. / Santelli, E. / Chung, T.D.Y. / ...Authors: Stanford, S.M. / Diaz, M.A. / Ardecky, R.J. / Zou, J. / Roosild, T. / Holmes, Z.J. / Nguyen, T.P. / Hedrick, M.P. / Rodiles, S. / Guan, A. / Grotegut, S. / Santelli, E. / Chung, T.D.Y. / Jackson, M.R. / Bottini, N. / Pinkerton, A.B.
History
DepositionOct 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low molecular weight phosphotyrosine protein phosphatase
B: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6096
Polymers35,7162
Non-polymers8934
Water8,395466
1
A: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3053
Polymers17,8581
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Low molecular weight phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3053
Polymers17,8581
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.971, 58.960, 95.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase / LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red ...LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase 1


Mass: 17858.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Codon+
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-WE7 / 3-[(2,6-dichlorophenyl)methyl]-8-(2-methylphenyl)-3H-purin-6-amine


Mass: 384.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15Cl2N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 3350, Potassium Nitrate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 72357 / % possible obs: 94.1 % / Redundancy: 9.5 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.078 / Net I/σ(I): 11.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4521 / CC1/2: 0.909 / CC star: 0.976 / Rpim(I) all: 0.134 / Rrim(I) all: 0.302 / Χ2: 1.07 / % possible all: 59.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jnr

5jnr


Resolution: 1.3→47.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.205 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 3739 5.2 %RANDOM
Rwork0.1254 ---
obs0.1273 68550 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 242.26 Å2 / Biso mean: 18.557 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.3→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 74 466 3006
Biso mean--14.64 32.21 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182432
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6923722
X-RAY DIFFRACTIONr_angle_other_deg1.5261.6015676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.11322.089158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28815476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6881522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023167
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02611
X-RAY DIFFRACTIONr_rigid_bond_restr14.09435166
LS refinement shellResolution: 1.304→1.338 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 210 -
Rwork0.27 3431 -
all-3641 -
obs--65.56 %

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