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- PDB-8v6w: Crystal structure of the core catalytic domain of human inositol ... -

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Basic information

Entry
Database: PDB / ID: 8v6w
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 1
ComponentsInositol polyphosphate multikinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structure-based inhibitor development / kinase / inhibitor / inositol polyphosphate / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-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 / ciliary basal body / nucleoplasm / ATP binding / metal ion binding / nucleus / 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: 1.95 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)30,1212
Polymers29,8281
Non-polymers2931
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.656, 77.656, 84.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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
Details: UNC7437 / Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NFU5, inositol-polyphosphate multikinase
#2: Chemical ChemComp-YHE / (2E)-3-[3-(3,5-dimethylphenyl)-2,1-benzoxazol-5-yl]prop-2-enoic acid


Mass: 293.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
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 10 mM compound 1 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: Mar 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 19525 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 0.951 / CC star: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Χ2: 1.088 / Net I/σ(I): 19.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 962 / CC1/2: 0.826 / CC star: 0.998 / Rpim(I) all: 0.245 / Rrim(I) all: 0.816 / Χ2: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→37.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.91 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22771 1000 5.2 %RANDOM
Rwork0.16204 ---
obs0.16532 18364 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.657 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å20 Å2
2--1.06 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 1.95→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 110 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122017
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161817
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6682732
X-RAY DIFFRACTIONr_angle_other_deg0.3991.5784244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.50959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79310346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
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_it5.1522.937952
X-RAY DIFFRACTIONr_mcbond_other5.1432.937951
X-RAY DIFFRACTIONr_mcangle_it6.7414.4081187
X-RAY DIFFRACTIONr_mcangle_other6.744.4111188
X-RAY DIFFRACTIONr_scbond_it5.2223.2971065
X-RAY DIFFRACTIONr_scbond_other5.2193.2971066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.784.811546
X-RAY DIFFRACTIONr_long_range_B_refined8.85941.5232380
X-RAY DIFFRACTIONr_long_range_B_other8.70939.9192354
X-RAY DIFFRACTIONr_rigid_bond_restr11.34133834
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 58 -
Rwork0.195 1257 -
obs--94.2 %
Refinement TLS params.Method: refined / Origin x: 3.3939 Å / Origin y: 17.8895 Å / Origin z: 25.4063 Å
111213212223313233
T0.0027 Å2-0.0012 Å2-0.0031 Å2-0.0073 Å20.0032 Å2--0.023 Å2
L0.1096 °2-0.0413 °2-0.0572 °2-0.0418 °20.039 °2--0.1396 °2
S-0.0111 Å °0.0106 Å °0.0012 Å °0.0039 Å °0.0068 Å °-0.006 Å °0.0066 Å °0.0015 Å °0.0043 Å °

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