Structure of PDB 6e08 Chain L Binding Site BS01

Receptor Information
>6e08 Chain L (length=486) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSDTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLPENTFIVGYARSRLTV
ADIRKQSEPFFKATPEEKLKLEDFFARNSYVAGQYDDAASYQRLNSHMNA
LHLGSQANRLFYLALPPTVYEAVTKNIHESCMSQIGWNRIIVEKPFGRDL
QSSDRLSNHISSLFREDQIYRIDHYLGKEMVQNLMVLRFANRIFGPIWNR
DNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPA
STNSDDVRDEKVKVLKCISEVQANNVVLGQYVGNPDGEGEATKGYLDDPT
VPRGSTTATFAAVVLYVENERWDGVPFILRCGKALNERKAEVRLQFHDVA
GDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESELDLTYGNR
YKNVKLPDAYERLILDVFCGSQMHFVRSDELREAWRIFTPLLHQIELEKP
KPIPYIYGSRGPTEADELMKRVGFQYEGTYKWVNPH
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 chain6e08 Chain L Residue 601 [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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PDB6e08 Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K238 K366 R370 R393 Y401 K403 D421 R487 D493 M496 F501 Y503 Y507 W509
Binding residue
(residue number reindexed from 1)		K211 K339 R343 R366 Y374 K376 D394 R460 D466 M469 F474 Y476 Y480 W482
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.49: glucose-6-phosphate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0004345 glucose-6-phosphate dehydrogenase activity
GO:0005515 protein binding
GO:0005536 D-glucose binding
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0030246 carbohydrate binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0050661 NADP binding
Biological Process
GO:0006006 glucose metabolic process
GO:0006098 pentose-phosphate shunt
GO:0006629 lipid metabolic process
GO:0006695 cholesterol biosynthetic process
GO:0006739 NADP metabolic process
GO:0006740 NADPH regeneration
GO:0006749 glutathione metabolic process
GO:0009051 pentose-phosphate shunt, oxidative branch
GO:0010041 response to iron(III) ion
GO:0010734 negative regulation of protein glutathionylation
GO:0014070 response to organic cyclic compound
GO:0019322 pentose biosynthetic process
GO:0021762 substantia nigra development
GO:0032094 response to food
GO:0034599 cellular response to oxidative stress
GO:0043249 erythrocyte maturation
GO:0043523 regulation of neuron apoptotic process
GO:0045471 response to ethanol
GO:0046390 ribose phosphate biosynthetic process
GO:0051156 glucose 6-phosphate metabolic process
GO:0061052 negative regulation of cell growth involved in cardiac muscle cell development
GO:1904879 positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
GO:2000378 negative regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009898 cytoplasmic side of plasma membrane
GO:0016020 membrane
GO:0034451 centriolar satellite
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6e08, PDBe:6e08, PDBj:6e08
PDBsum6e08
PubMed30279493
UniProtP11413|G6PD_HUMAN Glucose-6-phosphate 1-dehydrogenase (Gene Name=G6PD)

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