Structure of PDB 5wbr Chain B Binding Site BS01

Receptor Information
>5wbr Chain B (length=301) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLVPRGSQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSC
TVLSLLGAPCAFMGSMAPGHVADFLVADFRRRGVDVSQVAWQSKGDTPSS
CCIINNSNGNRTIVLHDTSLPDVSATDFEKVDLTQFKWIHIEGRNASEQV
KMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAK
HLGFQSAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPP
PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGI
V
Ligand information
Ligand IDA3Y
InChIInChI=1S/C19H26F3N5O2/c20-19(21,22)16-10-17(26-6-4-25(5-7-26)8-9-28)24-18(15(16)11-23)27-3-1-2-14(12-27)13-29/h10,14,28-29H,1-9,12-13H2/t14-/m0/s1
InChIKeyXNJVLRJGPUMHDH-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c(c(c(nc1N2CCN(CC2)CCO)N3CCC[C@@H](C3)CO)C#N)C(F)(F)F
CACTVS 3.385OCCN1CCN(CC1)c2cc(c(C#N)c(n2)N3CCC[C@H](CO)C3)C(F)(F)F
ACDLabs 12.01N3(CCN(c2cc(C(F)(F)F)c(c(N1CC(CCC1)CO)n2)C#N)CC3)CCO
OpenEye OEToolkits 2.0.6c1c(c(c(nc1N2CCN(CC2)CCO)N3CCCC(C3)CO)C#N)C(F)(F)F
CACTVS 3.385OCCN1CCN(CC1)c2cc(c(C#N)c(n2)N3CCC[CH](CO)C3)C(F)(F)F
FormulaC19 H26 F3 N5 O2
Name6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain5wbr Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5wbr Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).
Resolution2.58 Å
Binding residue
(original residue number in PDB)		A224 A226 T253 G257 C289
Binding residue
(residue number reindexed from 1)		A227 A229 T256 G260 C292
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.77,IC50=16.79uM
BindingDB: IC50=16790nM
Enzymatic activity
Catalytic site (original residue number in PDB) G255 A256 G257 D258
Catalytic site (residue number reindexed from 1) G258 A259 G260 D261
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:5wbr, PDBe:5wbr, PDBj:5wbr
PDBsum5wbr
PubMed28853885
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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