Structure of PDB 5wbo Chain A Binding Site BS01

Receptor Information
>5wbo Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTVLSL
LGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSSCCIIN
NSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQR
IDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ
SAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVD
TLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV
Ligand information
Ligand IDA1Y
InChIInChI=1S/C12H15N3O/c1-9-7-10(2)14-12(11(9)8-13)15-3-5-16-6-4-15/h7H,3-6H2,1-2H3
InChIKeyLUTZBWBXBMVIOV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(nc(c1C#N)N2CCOCC2)C
CACTVS 3.385Cc1cc(C)c(C#N)c(n1)N2CCOCC2
ACDLabs 12.01N2(c1c(C#N)c(C)cc(C)n1)CCOCC2
FormulaC12 H15 N3 O
Name4,6-dimethyl-2-(morpholin-4-yl)pyridine-3-carbonitrile
ChEMBLCHEMBL1500542
DrugBank
ZINCZINC000019117525
PDB chain5wbo Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5wbo Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).
Resolution2.25 Å
Binding residue
(original residue number in PDB)		A226 F260
Binding residue
(residue number reindexed from 1)		A224 F258
Annotation score1
Binding affinityMOAD: Kd=62uM
PDBbind-CN: -logKd/Ki=4.21,Kd=62uM
BindingDB: Kd=62000nM,IC50=319000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G255 A256 G257 D258
Catalytic site (residue number reindexed from 1) G253 A254 G255 D256
Enzyme Commision number 2.7.1.3: ketohexokinase.
Gene Ontology
Molecular Function
GO:0004454 ketohexokinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0070061 fructose binding
Biological Process
GO:0006000 fructose metabolic process
GO:0006796 phosphate-containing compound metabolic process
GO:0009744 response to sucrose
GO:0009749 response to glucose
GO:0009750 response to fructose
GO:0010043 response to zinc ion
GO:0016310 phosphorylation
GO:0032868 response to insulin
GO:0046835 carbohydrate phosphorylation
GO:0070873 regulation of glycogen metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wbo, PDBe:5wbo, PDBj:5wbo
PDBsum5wbo
PubMed28853885
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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