Structure of PDB 4yrw Chain A Binding Site BS05

Receptor Information
>4yrw Chain A (length=1289) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADELVFFVNGKKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEGGCGACT
VMISKYDRLQNKIVHFSVNACLAPICSLHHVAVTTVEGIGNTQKLHPVQE
RIARSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIENAFQGNLCRCTGY
RPILQGFRTFAKDLSPSLFNPEDFKPLDPTQEPIFPPELLRLKDTPQKKL
RFEGERVTWIQASTMEELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPL
IVCPAWIPELNSVVHGPEGISFGASCPLSLVESVLAEEIAKLPEQKTEVF
RGVMEQLRWFAGKQVKSVASIGGNIITASPISDLNPVFMASGAKLTLVSR
GTRRTVRMDHTFFPGYRKTLLRPEEILLSIEIPYSKEGEFFSAFKQASRR
EDDIAKVTSGMRVLFKPGTIEVQELSLCFGGMADRTISALKTTPKQLSKS
WNEELLQSVCAGLAEELQLAPDAPGGMVEFRRTLTLSFFFKFYLTVLQKL
GRADLEDMCGKLDPTFASATLLFQKDPPANVQLFQEVPKDQSEEDMVGRP
LPHLAANMQASGEAVYCDDIPRYENELSLRLVTSTRAHAKITSIDTSEAK
KVPGFVCFLTAEDVPNSNATGLFNDETVFAKDEVTCVGHIIGAVVADTPE
HAQRAARGVKITYEDLPAIITIQDAINNNSFYGSEIKIEKGDLKKGFSEA
DNVVSGELYIGGQEHFYLETNCTIAVPKGEAGEMELFVSTQNTMKTQSFV
AKMLGVPDNRIVVRVKRMGGGFGGKETRSTVVSTALALAAHKTGRPVRCM
LDRDEDMLITGGRHPFLAKYKVGFMKTGTVVALEVAHFSNGGNTEDLSRS
IMERALFHMDNAYKIPNIRGTGRICKTNLPSNTAFRGFGGPQGMLIAEYW
MSEVAITCGLPAEEVRRKNMYKEGDLTHFNQKLEGFTLPRCWDECIASSQ
YLARKREVEKFNRENCWKKRGLCIIPTKFGISFTLPFLNQGGALVHVYTD
GSVLLTHGGTEMGQGLHTKMVQVASRALKIPTSKIHISETSTNTVPNTSP
TAASASADLNGQGVYEACQTILKRLEPFKKKKPTGPWEAWVMDAYTSAVS
LSATGFYKTPNLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRT
DIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTMEELHYSPEGSLHTRGPST
YKIPAFGSIPIEFRVSLLRDCPNKRAIYASKAVGEPPLFLASSIFFAIKD
AIRAARAQHGDNAKQLFQLDSPATPEKIRNACVDQFTTL
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4yrw Chain A Residue 3005 [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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PDB4yrw 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)		G46 K255 L256 V257 V258 G259 N260 T261 E262 I263 F336 A337 A345 S346 G349 N350 I352 T353 S358 D359 I402 L403
Binding residue
(residue number reindexed from 1)		G44 K229 L230 V231 V232 G233 N234 T235 E236 I237 F310 A311 A319 S320 G323 N324 I326 T327 S332 D333 I376 L377
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Q767 E802 R880 H884 R912 G1260 E1261
Catalytic site (residue number reindexed from 1) Q741 E776 R854 H858 R886 G1234 E1235
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:4yrw, PDBe:4yrw, PDBj:4yrw
PDBsum4yrw
PubMed25817260
UniProtP22985|XDH_RAT Xanthine dehydrogenase/oxidase (Gene Name=Xdh)

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