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- PDB-6gl3: Crystal structure of human Phosphatidylinositol 4-kinase III beta... -

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Basic information

Entry
Database: PDB / ID: 6gl3
TitleCrystal structure of human Phosphatidylinositol 4-kinase III beta (PI4KIIIbeta) in complex with ligand 44
ComponentsPhosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
KeywordsIMMUNE SYSTEM / PI4K KINASE / Immunosuppressive / Phosphoinositol 4-kinase IIIbeta / transplantation / human mixed lymphocyte reaction / selectivity profile / binding mode / solubility
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / lysosome organization / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / lysosome organization / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding / receptor-mediated endocytosis / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain ...: / PI4KB/PIK1, accessory (PIK) domain / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-EMW / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsLammens, A. / Augustin, M. / Steinbacher, S. / Reuberson, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of a Potent, Orally Bioavailable PI4KIII beta Inhibitor (UCB9608) Able To Significantly Prolong Allogeneic Organ Engraftment in Vivo.
Authors: Reuberson, J. / Horsley, H. / Franklin, R.J. / Ford, D. / Neuss, J. / Brookings, D. / Huang, Q. / Vanderhoydonck, B. / Gao, L.J. / Jang, M.Y. / Herdewijn, P. / Ghawalkar, A. / Fallah-Arani, ...Authors: Reuberson, J. / Horsley, H. / Franklin, R.J. / Ford, D. / Neuss, J. / Brookings, D. / Huang, Q. / Vanderhoydonck, B. / Gao, L.J. / Jang, M.Y. / Herdewijn, P. / Ghawalkar, A. / Fallah-Arani, F. / Khan, A.R. / Henshall, J. / Jairaj, M. / Malcolm, S. / Ward, E. / Shuttleworth, L. / Lin, Y. / Li, S. / Louat, T. / Waer, M. / Herman, J. / Payne, A. / Ceska, T. / Doyle, C. / Pitt, W. / Calmiano, M. / Augustin, M. / Steinbacher, S. / Lammens, A. / Allen, R.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
B: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3883
Polymers87,9772
Non-polymers4101
Water27015
1
A: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3992
Polymers43,9891
Non-polymers4101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)43,9891
Polymers43,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.468, 69.484, 172.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta / PtdIns 4-kinase beta / NPIK / PI4K92


Mass: 43988.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase
#2: Chemical ChemComp-EMW / (3~{S})-4-(6-azanyl-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl)-~{N}-(4-methoxy-2-methyl-phenyl)-3-methyl-piperazine-1-carboxamide


Mass: 410.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium citrate, 22% (w/v) PEG3350, 10 mM Manganese(II)chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→86.42 Å / Num. obs: 19839 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.997 / Net I/σ(I): 15.05
Reflection shellResolution: 2.77→2.842 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.72 / Num. unique obs: 1398 / CC1/2: 0.804 / % possible all: 98.85

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→86.42 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.333 --
Rwork0.276 --
obs0.278 742 97 %
all-19097 -
Refinement stepCycle: LAST / Resolution: 2.77→86.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 30 15 5333

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