Structure of PDB 5wbz Chain A Binding Site BS01

Receptor Information

>5wbz 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 ID

A4J

InChI

InChI=1S/C16H19F3N4O3/c1-15(26)2-3-22(8-15)14-9(5-20)10(16(17,18)19)4-13(21-14)23-6-11(24)12(25)7-23/h4,11-12,24-26H,2-3,6-8H2,1H3/t11-,12-,15-/m0/s1

InChIKey

FAXXYODRCHXHTQ-HUBLWGQQSA-N

SMILES

Software	SMILES
CACTVS 3.385	C[C]1(O)CCN(C1)c2nc(cc(c2C#N)C(F)(F)F)N3C[CH](O)[CH](O)C3
CACTVS 3.385	C[C@]1(O)CCN(C1)c2nc(cc(c2C#N)C(F)(F)F)N3C[C@H](O)[C@@H](O)C3
ACDLabs 12.01	N1(CC(C(O)C1)O)c2nc(c(c(c2)C(F)(F)F)C#N)N3CCC(C)(C3)O
OpenEye OEToolkits 2.0.6	CC1(CCN(C1)c2c(c(cc(n2)N3CC(C(C3)O)O)C(F)(F)F)C#N)O
OpenEye OEToolkits 2.0.6	C[C@@]1(CCN(C1)c2c(c(cc(n2)N3C[C@@H]([C@H](C3)O)O)C(F)(F)F)C#N)O

Formula

C16 H19 F3 N4 O3

Name

6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile

PDB chain

5wbz 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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Structure summary

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PDB	5wbz Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).
Resolution	2.4 Å
Binding residue (original residue number in PDB)	N107 A224 A226 E227 P246 A256 G257 F260 G286 C289
Binding residue (residue number reindexed from 1)	N105 A222 A224 E225 P244 A254 G255 F258 G284 C287
Annotation score	1
Binding affinity	MOAD: ic50=0.39uM PDBbind-CN: -logKd/Ki=6.41,IC50=0.39uM BindingDB: IC50=450nM

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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Cellular Component

External links

PDB	RCSB:5wbz, PDBe:5wbz, PDBj:5wbz
PDBsum	5wbz
PubMed	28853885
UniProt	P50053\|KHK_HUMAN Ketohexokinase (Gene Name=KHK)

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