Structure of PDB 3nc9 Chain A Binding Site BS01

Receptor Information
>3nc9 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 IDTR3
InChIInChI=1S/C20H22N4OS/c1-26-20-17-8-7-15(22-19(25)14-9-11-21-12-10-14)13-18(17)24(23-20)16-5-3-2-4-6-16/h2-8,13-14,21H,9-12H2,1H3,(H,22,25)
InChIKeyDHDKYDLNUPJXFQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CSc1c2ccc(cc2n(n1)c3ccccc3)NC(=O)C4CCNCC4
ACDLabs 12.01O=C(Nc1ccc2c(c1)n(nc2SC)c3ccccc3)C4CCNCC4
CACTVS 3.370CSc1nn(c2ccccc2)c3cc(NC(=O)C4CCNCC4)ccc13
FormulaC20 H22 N4 O S
NameN-[3-(methylsulfanyl)-1-phenyl-1H-indazol-6-yl]piperidine-4-carboxamide
ChEMBLCHEMBL1236391
DrugBank
ZINCZINC000058638372
PDB chain3nc9 Chain B Residue 299 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nc9 Electron density guided fragment-based lead discovery of ketohexokinase inhibitors.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A226 E227 G229 P246 A256 F260 C282 A285 C289
Binding residue
(residue number reindexed from 1)		A224 E225 G227 P244 A254 F258 C280 A283 C287
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.48,IC50=330nM
BindingDB: IC50=590nM
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:3nc9, PDBe:3nc9, PDBj:3nc9
PDBsum3nc9
PubMed21033679
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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