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- PDB-8v6z: Crystal structure of the core catalytic domain of human inositol ... -

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Basic information

Entry
Database: PDB / ID: 8v6z
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 4
ComponentsInositol polyphosphate multikinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structure-based inhibitor development / kinase / inhibitor / inositol polyphosphate / inositol polyphosphate kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity ...Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
: / Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046 United States
CitationJournal: To Be Published
Title: Structure-based development of IPMK kinase inhibitors.
Authors: Wang, H. / Shears, S.B.
History
DepositionDec 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1192
Polymers29,8281
Non-polymers2911
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.940, 77.940, 85.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

21A-743-

HOH

31A-745-

HOH

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Components

#1: Protein Inositol polyphosphate multikinase / Inositol 1 / 3 / 4 / 6-tetrakisphosphate 5-kinase


Mass: 29827.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IPMK, IMPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NFU5, inositol-tetrakisphosphate 5-kinase, inositol-polyphosphate multikinase, phosphatidylinositol-4,5-bisphosphate 3-kinase
#2: Chemical ChemComp-YHS / (5P)-3-(3,5-dimethylphenyl)-5-(1H-tetrazol-5-yl)-2,1-benzoxazole


Mass: 291.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 2 mM compound 4 for 3 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23240 / % possible obs: 99.1 % / Redundancy: 11.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.119 / Χ2: 1.145 / Net I/σ(I): 20.39
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 1136 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.268 / Rrim(I) all: 0.819 / Χ2: 0.636 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→46.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.037 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22942 1162 5.1 %RANDOM
Rwork0.17294 ---
obs0.17576 21483 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.625 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å20 Å2
2--1.49 Å2-0 Å2
3----2.97 Å2
Refinement stepCycle: 1 / Resolution: 1.85→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 22 157 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122050
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161835
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.6682783
X-RAY DIFFRACTIONr_angle_other_deg0.311.5784293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.50159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81810350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0420.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6462.292976
X-RAY DIFFRACTIONr_mcbond_other1.6452.292976
X-RAY DIFFRACTIONr_mcangle_it2.3483.4291225
X-RAY DIFFRACTIONr_mcangle_other2.3473.431226
X-RAY DIFFRACTIONr_scbond_it1.7522.5811074
X-RAY DIFFRACTIONr_scbond_other1.7512.5811073
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.313.7821559
X-RAY DIFFRACTIONr_long_range_B_refined3.93545.6848852
X-RAY DIFFRACTIONr_long_range_B_other3.744.8318746
X-RAY DIFFRACTIONr_rigid_bond_restr3.09633885
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 87 -
Rwork0.221 1432 -
obs--90.47 %
Refinement TLS params.Method: refined / Origin x: 3.32 Å / Origin y: 17.999 Å / Origin z: 25.682 Å
111213212223313233
T0.0013 Å20.0004 Å2-0.0005 Å2-0.0014 Å20.0001 Å2--0.0295 Å2
L0.1082 °20.0129 °2-0.0325 °2-0.0399 °2-0.0113 °2--0.0686 °2
S-0.0028 Å °0.0067 Å °0.0014 Å °0.0061 Å °0.0025 Å °0.0016 Å °0.0018 Å °-0.0014 Å °0.0004 Å °

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