Structure of PDB 5wbm Chain A Binding Site BS01

Receptor Information
>5wbm 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 IDA4G
InChIInChI=1S/C13H18N4O/c1-9-5-14-12-11(9)13(16-8-15-12)17-4-2-3-10(6-17)7-18/h5,8,10,18H,2-4,6-7H2,1H3,(H,14,15,16)/t10-/m1/s1
InChIKeyYDGQZYCXWPQCTM-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c[nH]c2ncnc(N3CCC[C@@H](CO)C3)c12
ACDLabs 12.01n2c1ncc(C)c1c(nc2)N3CCCC(CO)C3
OpenEye OEToolkits 2.0.6Cc1c[nH]c2c1c(ncn2)N3CCCC(C3)CO
OpenEye OEToolkits 2.0.6Cc1c[nH]c2c1c(ncn2)N3CCC[C@H](C3)CO
CACTVS 3.385Cc1c[nH]c2ncnc(N3CCC[CH](CO)C3)c12
FormulaC13 H18 N4 O
Name[(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]methanol
ChEMBLCHEMBL4086173
DrugBank
ZINC
PDB chain5wbm 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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PDB5wbm Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).
Resolution2.16 Å
Binding residue
(original residue number in PDB)		A226 G229 A230 C282 C289
Binding residue
(residue number reindexed from 1)		A224 G227 A228 C280 C287
Annotation score1
Binding affinityMOAD: Kd=20uM
PDBbind-CN: -logKd/Ki=4.70,Kd=20uM
BindingDB: IC50=120226nM,Kd=20000nM
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:5wbm, PDBe:5wbm, PDBj:5wbm
PDBsum5wbm
PubMed28853885
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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