Structure of PDB 3nc9 Chain B Binding Site BS01

Receptor Information
>3nc9 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 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 300 [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 G229 P246 A256
Binding residue
(residue number reindexed from 1)		A229 G232 P249 A259
Annotation score1
Binding affinityMOAD: ic50=330nM
PDBbind-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) 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:3nc9, PDBe:3nc9, PDBj:3nc9
PDBsum3nc9
PubMed21033679
UniProtP50053|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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