Structure of PDB 3dn5 Chain A Binding Site BS01

Receptor Information
>3dn5 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
LSCTSHKDYPFHEEF
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain3dn5 Chain A Residue 500 [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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PDB3dn5 Structure-Based Optimization of Aldose Reductase Inhibitors Originating from Virtual Screening
Resolution1.45 Å
Binding residue
(original residue number in PDB)		G18 T19 W20 K21 D43 Y48 H110 N160 Q183 Y209 S210 P211 L212 S214 P215 D216 A245 I260 P261 K262 S263 T265 R268 E271 N272 C298
Binding residue
(residue number reindexed from 1)		G18 T19 W20 K21 D43 Y48 H110 N160 Q183 Y209 S210 P211 L212 S214 P215 D216 A245 I260 P261 K262 S263 T265 R268 E271 N272 C298
Annotation score4
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dn5, PDBe:3dn5, PDBj:3dn5
PDBsum3dn5
PubMed19301313
UniProtP15121|ALDR_HUMAN Aldo-keto reductase family 1 member B1 (Gene Name=AKR1B1)

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