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- PDB-13lz: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinas... -

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Basic information

Entry
Database: PDB / ID: 13lz
TitleCrystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in Complex with an Inhibitor NCGC00879727
ComponentsInositol-tetrakisphosphate 1-kinase
KeywordsTRANSFERASE / inhibitor development / inositol phosphate kinase / inhibitor complex / cancer therapy
Function / homology
Function and homology information


inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development ...inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development / necroptotic process / Synthesis of IP3 and IP4 in the cytosol / catalytic activity / isomerase activity / blood coagulation / Factors involved in megakaryocyte development and platelet production / apical plasma membrane / hydrolase activity / magnesium ion binding / signal transduction / ATP binding / cytosol
Similarity search - Function
Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
: / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES103340 United States
CitationJournal: Slas Discov / Year: 2026
Title: A Hybrid Experimental and in silico Platform for ITPK1 Chemical Probe Discovery.
Authors: Yasgar, A. / Jain, S. / Wang, H. / Lee, C.S. / Zong, G. / Zhang, H. / Lindberg, E. / Woodroofe, C. / Lane, K. / Blackman, B. / Crook, D. / Lin, H. / Baljinnyam, B. / Ronzetti, M. / Simeonov, ...Authors: Yasgar, A. / Jain, S. / Wang, H. / Lee, C.S. / Zong, G. / Zhang, H. / Lindberg, E. / Woodroofe, C. / Lane, K. / Blackman, B. / Crook, D. / Lin, H. / Baljinnyam, B. / Ronzetti, M. / Simeonov, A. / Rana, S. / Rai, G. / Shears, S. / Stanley, R.E. / Zakharov, A.V. / Luo, J. / Martinez, N.J.
History
DepositionMay 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-tetrakisphosphate 1-kinase
B: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,70811
Polymers74,6092
Non-polymers1,0999
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7104
Polymers37,3041
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.757, 126.219, 63.029
Angle α, β, γ (deg.)90.000, 90.117, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Inositol-tetrakisphosphate 1-kinase / Inositol 1 / 3 / 4-trisphosphate 5/6-kinase / Inositol-triphosphate 5/6-kinase / Ins(1 / 4)P(3) 5/6-kinase


Mass: 37304.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13572, inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase
#2: Chemical ChemComp-A1DHL / N-ethyl[1]benzofuro[3,2-d]pyrimidin-4-amine


Mass: 213.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 41.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Hanging drops comprised 2 ul of 14 mg/mL protein solution and 2 ul of well buffer (21% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, and 10% Glycerol) that was present in the ...Details: Hanging drops comprised 2 ul of 14 mg/mL protein solution and 2 ul of well buffer (21% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, and 10% Glycerol) that was present in the reservoir. Crystal complexes with inhibitors were formed in a soaking buffer (25% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, 20% Glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→33.66 Å / Num. obs: 31194 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.47 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.083 / Rrim(I) all: 0.153 / Net I/σ(I): 6.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1 / Num. unique obs: 1526 / CC1/2: 0.318 / Rpim(I) all: 0.818 / Rrim(I) all: 1.477 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.66 Å / SU ML: 0.3419 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 1498 4.8 %
Rwork0.2149 29691 -
obs0.2165 31189 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5085 0 67 160 5312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225246
X-RAY DIFFRACTIONf_angle_d0.49987106
X-RAY DIFFRACTIONf_chiral_restr0.0443800
X-RAY DIFFRACTIONf_plane_restr0.0043919
X-RAY DIFFRACTIONf_dihedral_angle_d13.23371949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.3421150.31852668X-RAY DIFFRACTION98.93
2.27-2.350.33961550.30392701X-RAY DIFFRACTION99.1
2.35-2.450.31051610.28612676X-RAY DIFFRACTION99.23
2.45-2.560.30071520.27342646X-RAY DIFFRACTION99.33
2.56-2.690.30221460.26572707X-RAY DIFFRACTION99.62
2.69-2.860.32961160.25482762X-RAY DIFFRACTION99.55
2.86-3.080.27831510.24332686X-RAY DIFFRACTION99.44
3.08-3.390.26421240.21142707X-RAY DIFFRACTION98.74
3.39-3.880.22441450.18522676X-RAY DIFFRACTION98.81
3.88-4.890.1791260.16762719X-RAY DIFFRACTION98.51
4.89-33.660.22011070.18662743X-RAY DIFFRACTION98.34
Refinement TLS params.Method: refined / Origin x: 17.822280207323 Å / Origin y: 0.62389259040146 Å / Origin z: 42.364672614558 Å
111213212223313233
T0.2453377596234 Å2-0.027709298343848 Å20.010226996208495 Å2-0.29029713404417 Å2-0.033498956161987 Å2--0.25553789114178 Å2
L1.0823615969535 °2-0.24669803748053 °20.20181347124437 °2-0.72560260693178 °2-0.14136257316313 °2--0.33693532613228 °2
S0.0090671737646898 Å °-0.14128665727489 Å °0.028708840233453 Å °0.08720344074362 Å °0.03505197215886 Å °-0.029918349296942 Å °-0.024004578522464 Å °0.0078472654067186 Å °-0.040346938733112 Å °
Refinement TLS groupSelection details: all

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