Structure of PDB 4ysw Chain B Binding Site BS05

Receptor Information
>4ysw Chain B (length=1286) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADELVFFVNGKKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEGGCGACT
VMISKYDRLQNKIVHFSVNACLAPICSLHHVAVTTVEGIGNTQKLHPVQE
RIARSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIENAFQGNLCRCTGY
RPILQGFRTFAKPSLFNPEDFKPLDPTQEPIFPPELLRLKDTPQKKLRFE
GERVTWIQASTMEELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPLIVC
PAWIPELNSVVHGPEGISFGASCPLSLVESVLAEEIAKLPEQKTEVFRGV
MEQLRWFAGKQVKSVASIGGNIITASPISDLNPVFMASGAKLTLVSRGTR
RTVRMDHTFFPGYRKTLLRPEEILLSIEIPYSKEGEFFSAFKQASRREDD
IAKVTSGMRVLFKPGTIEVQELSLCFGGMADRTISALKTTPKQLSKSWNE
ELLQSVCAGLAEELQLAPDAPGGMVEFRRTLTLSFFFKFYLTVLQKLGRA
DLEDMCGKLDPTFASATLLFQKDPPANVQLFQEVPKDQSEEDMVGRPLPH
LAANMQASGEAVYCDDIPRYENELSLRLVTSTRAHAKITSIDTSEAKKVP
GFVCFLTAEDVPNSNATGLFNDETVFAKDEVTCVGHIIGAVVADTPEHAQ
RAARGVKITYEDLPAIITIQDAINNNSFYGSEIKIEKGDLKKGFSEADNV
VSGELYIGGQEHFYLETNCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKM
LGVPDNRIVVRVKRMGGGFGGKETRSTVVSTALALAAHKTGRPVRCMLDR
DEDMLITGGRHPFLAKYKVGFMKTGTVVALEVAHFSNGGNTEDLSRSIME
RALFHMDNAYKIPNIRGTGRICKTNLPSNTAFRGFGGPQGMLIAEYWMSE
VAITCGLPAEEVRRKNMYKEGDLTHFNQKLEGFTLPRCWDECIASSQYLA
RKREVEKFNRENCWKKRGLCIIPTKFGISFTLPFLNQGGALVHVYTDGSV
LLTHGGTEMGQGLHTKMVQVASRALKIPTSKIHISETSTNTVPNTSPTAA
SASADLNGQGVYEACQTILKRLEPFKKKKPTGPWEAWVMDAYTSAVSLSA
TGFYKTPNLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIV
MDVGSSLNPAIDIGQVEGAFVQGLGLFTMEELHYSPEGSLHTRGPSTYKI
PAFGSIPIEFRVSLLRDCPNKRAIYASKAVGEPPLFLASSIFFAIKDAIR
AARAQHGDNAKQLFQLDSPATPEKIRNACVDQFTTL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain4ysw Chain B Residue 4005 [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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PDB4ysw The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		E262 K270 S355 P356 I357 Y392 R393 D429 I430 G457 A459 D460 P500 R507 S1225
Binding residue
(residue number reindexed from 1)		E233 K241 S326 P327 I328 Y363 R364 D400 I401 G428 A430 D431 P471 R478 S1196
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Q767 E802 R880 H884 R912 G1260 E1261
Catalytic site (residue number reindexed from 1) Q738 E773 R851 H855 R883 G1231 E1232
Enzyme Commision number 1.17.1.4: xanthine dehydrogenase.
1.17.3.2: xanthine oxidase.
Gene Ontology
Molecular Function
GO:0004854 xanthine dehydrogenase activity
GO:0004855 xanthine oxidase activity
GO:0005506 iron ion binding
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0050421 nitrite reductase (NO-forming) activity
GO:0050660 flavin adenine dinucleotide binding
GO:0051536 iron-sulfur cluster binding
GO:0051537 2 iron, 2 sulfur cluster binding
GO:0070674 hypoxanthine dehydrogenase activity
GO:0070675 hypoxanthine oxidase activity
GO:0071949 FAD binding
Biological Process
GO:0000255 allantoin metabolic process
GO:0001937 negative regulation of endothelial cell proliferation
GO:0006147 guanine catabolic process
GO:0006148 inosine catabolic process
GO:0006149 deoxyinosine catabolic process
GO:0006154 adenosine catabolic process
GO:0006157 deoxyadenosine catabolic process
GO:0006161 deoxyguanosine catabolic process
GO:0006196 AMP catabolic process
GO:0006204 IMP catabolic process
GO:0007595 lactation
GO:0009114 hypoxanthine catabolic process
GO:0009115 xanthine catabolic process
GO:0010044 response to aluminum ion
GO:0010629 negative regulation of gene expression
GO:0016226 iron-sulfur cluster assembly
GO:0030856 regulation of epithelial cell differentiation
GO:0032496 response to lipopolysaccharide
GO:0034465 response to carbon monoxide
GO:0042542 response to hydrogen peroxide
GO:0043605 amide catabolic process
GO:0045602 negative regulation of endothelial cell differentiation
GO:0046038 GMP catabolic process
GO:0046055 dGMP catabolic process
GO:0046059 dAMP catabolic process
GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor
GO:0097184 response to azide
GO:1900745 positive regulation of p38MAPK cascade
GO:1900747 negative regulation of vascular endothelial growth factor signaling pathway
GO:2000379 positive regulation of reactive oxygen species metabolic process
GO:2001213 negative regulation of vasculogenesis
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005829 cytosol
GO:0016529 sarcoplasmic reticulum

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ysw, PDBe:4ysw, PDBj:4ysw
PDBsum4ysw
PubMed25817260
UniProtP22985|XDH_RAT Xanthine dehydrogenase/oxidase (Gene Name=Xdh)

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