Structure of PDB 2pdy Chain A Binding Site BS02

Receptor Information
>2pdy Chain A (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQN
ENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLK
LDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDE
GLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQ
SKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIR
FPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAL
LRDTSHKDYPFHEEF
Ligand information
Ligand IDFID
InChIInChI=1S/C12H10FN3O4/c13-5-1-2-7-6(3-5)12(4-8(20-7)9(14)17)10(18)15-11(19)16-12/h1-3,8H,4H2,(H2,14,17)(H2,15,16,18,19)/t8-,12-/m0/s1
InChIKeyWAAPEIZFCHNLKK-UFBFGSQYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Fc3ccc2OC(C(=O)N)CC1(C(=O)NC(=O)N1)c2c3
OpenEye OEToolkits 1.5.0c1cc2c(cc1F)[C@@]3(C[C@H](O2)C(=O)N)C(=O)NC(=O)N3
OpenEye OEToolkits 1.5.0c1cc2c(cc1F)C3(CC(O2)C(=O)N)C(=O)NC(=O)N3
CACTVS 3.341NC(=O)[CH]1C[C]2(NC(=O)NC2=O)c3cc(F)ccc3O1
CACTVS 3.341NC(=O)[C@@H]1C[C@]2(NC(=O)NC2=O)c3cc(F)ccc3O1
FormulaC12 H10 F N3 O4
Name(2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE;
FIDARESTAT
ChEMBLCHEMBL84446
DrugBankDB02021
ZINCZINC000003789766
PDB chain2pdy Chain A Residue 600 [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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PDB2pdy Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		W20 Y48 H110 W111 C298 L300
Binding residue
(residue number reindexed from 1)		W20 Y48 H110 W111 C298 L300
Annotation score1
Binding affinityMOAD: Kd=158nM
BindingDB: IC50=35nM,Kd=16nM
Enzymatic activity
Catalytic site (original residue number in PDB) D43 Y48 K77 H110
Catalytic site (residue number reindexed from 1) D43 Y48 K77 H110
Enzyme Commision number 1.1.1.21: aldose reductase.
1.1.1.300: NADP-retinol dehydrogenase.
1.1.1.372: D/L-glyceraldehyde reductase.
1.1.1.54: allyl-alcohol dehydrogenase.
Gene Ontology
Molecular Function
GO:0001758 retinal dehydrogenase activity
GO:0004032 aldose reductase (NADPH) activity
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0036130 prostaglandin H2 endoperoxidase reductase activity
GO:0043795 glyceraldehyde oxidoreductase activity
GO:0047655 allyl-alcohol dehydrogenase activity
GO:0047939 L-glucuronate reductase activity
GO:0047956 glycerol dehydrogenase (NADP+) activity
GO:0052650 all-trans-retinol dehydrogenase (NADP+) activity
Biological Process
GO:0001523 retinoid metabolic process
GO:0002070 epithelial cell maturation
GO:0003091 renal water homeostasis
GO:0005975 carbohydrate metabolic process
GO:0006629 lipid metabolic process
GO:0006693 prostaglandin metabolic process
GO:0006700 C21-steroid hormone biosynthetic process
GO:0019853 L-ascorbic acid biosynthetic process
GO:0035809 regulation of urine volume
GO:0042572 retinol metabolic process
GO:0043066 negative regulation of apoptotic process
GO:0044597 daunorubicin metabolic process
GO:0044598 doxorubicin metabolic process
GO:0046370 fructose biosynthetic process
GO:0071475 cellular hyperosmotic salinity response
GO:0072205 metanephric collecting duct development
Cellular Component
GO:0005615 extracellular space
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2pdy, PDBe:2pdy, PDBj:2pdy
PDBsum2pdy
PubMed18495158
UniProtP15121|ALDR_HUMAN Aldo-keto reductase family 1 member B1 (Gene Name=AKR1B1)

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