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- PDB-8omj: hKHK-C in complex with compound 28 -

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Basic information

Entry
Database: PDB / ID: 8omj
TitlehKHK-C in complex with compound 28
ComponentsKetohexokinase
KeywordsSUGAR BINDING PROTEIN / KHK / Ketohexokinase / sugar binding kinase / inhibitor complex
Function / homology
Function and homology information


Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / Fructose catabolism / ketohexokinase activity / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / Ketohexokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å
AuthorsPautsch, A. / Ebenhoch, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of BI-9787, a Potent Zwitterionic KHK-Inhibitor with Oral Bioavailability
Authors: Heine, N. / Weber, A. / Pautsch, A. / Gottschling, D. / Upheus, I. / Bauer, M. / Ebenhoch, R. / Nosse, B. / Kley, J.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketohexokinase
B: Ketohexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4006
Polymers68,1532
Non-polymers1,2474
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-51 kcal/mol
Surface area25040 Å2
Unit cell
Length a, b, c (Å)82.433, 83.379, 137.361
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ketohexokinase / Hepatic fructokinase


Mass: 34076.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Production host: Escherichia coli (E. coli) / References: UniProt: P50053, ketohexokinase
#2: Chemical ChemComp-VTM / [3-[[6-[(3~{a}~{R},6~{a}~{S})-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-pyrrolo[3,4-c]pyrrol-5-yl]-3-cyano-4-(trifluoromethyl)pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]methoxy-methyl-phosphinic acid


Mass: 527.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25F3N5O3PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 13% PEG 8000, 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.978→71.276 Å / Num. obs: 34330 / % possible obs: 93.5 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.06 / Net I/σ(I): 6.7
Reflection shellResolution: 1.978→2.221 Å / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1716 / Rsym value: 1.062 / % possible all: 8.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.978→20.9 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.309 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.335 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.238
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1382 -RANDOM
Rwork0.2091 ---
obs0.2108 34258 51.3 %-
Displacement parametersBiso mean: 44.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.1034 Å20 Å20 Å2
2--6.5559 Å20 Å2
3----3.4525 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.978→20.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 80 398 5057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936437HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1668SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes816HARMONIC5
X-RAY DIFFRACTIONt_it4749HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion589SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3942SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion17.46
LS refinement shellResolution: 1.98→2.12 Å
RfactorNum. reflection% reflection
Rfree0.3391 29 -
Rwork0.3113 --
obs0.3124 686 5.37 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7943-0.3654-0.43351.69640.70813.4620.112-0.1984-0.608-0.1984-0.07830.0705-0.6080.0705-0.03380.0085-0.00550.0254-0.0478-0.0032-0.04250.084812.615.6311
21.2636-0.1576-0.37960.7820.3731.17130.01720.0256-0.01950.0256-0.0338-0.0242-0.0195-0.02420.0167-0.12210.01030.02280.11690.0252-0.1154-12.202819.001458.1867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 298
2X-RAY DIFFRACTION2{ B|* }B-3 - 298

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