Structure of PDB 5wbq Chain B Binding Site BS01

Receptor Information
>5wbq 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 IDA3J
InChIInChI=1S/C16H17F3N4O/c1-3-9-6-11-12(21-9)13(23-5-4-15(2,24)8-23)10(7-20)14(22-11)16(17,18)19/h6,21,24H,3-5,8H2,1-2H3/t15-/m0/s1
InChIKeyPSWIJUOHBAWLCU-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCc1cc2c([nH]1)c(c(c(n2)C(F)(F)F)C#N)N3CC[C@](C3)(C)O
CACTVS 3.385CCc1[nH]c2c(c1)nc(c(C#N)c2N3CC[C@](C)(O)C3)C(F)(F)F
ACDLabs 12.01N#Cc1c(c2nc(cc2nc1C(F)(F)F)CC)N3CCC(C)(C3)O
OpenEye OEToolkits 2.0.6CCc1cc2c([nH]1)c(c(c(n2)C(F)(F)F)C#N)N3CCC(C3)(C)O
CACTVS 3.385CCc1[nH]c2c(c1)nc(c(C#N)c2N3CC[C](C)(O)C3)C(F)(F)F
FormulaC16 H17 F3 N4 O
Name2-ethyl-7-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-5-(trifluoromethyl)-1H-pyrrolo[3,2-b]pyridine-6-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain5wbq 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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PDB5wbq Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A224 A226 E227 P246 P247 A256 C289
Binding residue
(residue number reindexed from 1)		A227 A229 E230 P249 P250 A259 C292
Annotation score1
Binding affinityMOAD: ic50=1.48uM
PDBbind-CN: -logKd/Ki=5.83,IC50=1.47uM
BindingDB: IC50=1480nM
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5wbq, PDBe:5wbq, PDBj:5wbq
PDBsum5wbq
PubMed28853885
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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