Structure of PDB 3am9 Chain B Binding Site BS04

Receptor Information
>3am9 Chain B (length=1291) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACT
VMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTG
YRPILQGFRTFAKSPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLR
FEGERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMI
ICPAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFR
GVLEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRG
TRRTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRRE
DDIAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFW
NEKLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLG
KLDPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAAMQA
SGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLS
ADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVK
VTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYI
GGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNR
ILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLIT
GGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMD
NCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGL
PAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDK
FNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGT
EMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIY
GQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTP
NLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSL
NPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIP
TEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHT
NNNTKELFRLDSPATPEKIRNACVDKFTTLCVNCKPWSLRV
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 chain3am9 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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PDB3am9 FYX-051: A Novel and Potent Hybrid-Type Inhibitor of Xanthine Oxidoreductase
Resolution2.17 Å
Binding residue
(original residue number in PDB)		G46 L257 V258 G260 N261 T262 E263 I264 F337 S347 G350 N351 I353 T354 S359 D360 I403 L404
Binding residue
(residue number reindexed from 1)		G44 L229 V230 G232 N233 T234 E235 I236 F309 S319 G322 N323 I325 T326 S331 D332 I375 L376
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) Q731 E766 R844 H848 R876 G1224 E1225
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:0030151 molybdenum ion binding
GO:0042803 protein homodimerization activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0051536 iron-sulfur cluster binding
GO:0051537 2 iron, 2 sulfur cluster binding
GO:0071949 FAD binding
Biological Process
GO:0009115 xanthine catabolic process
Cellular Component
GO:0002197 xanthine dehydrogenase complex
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005777 peroxisome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3am9, PDBe:3am9, PDBj:3am9
PDBsum3am9
PubMed20952484
UniProtP80457|XDH_BOVIN Xanthine dehydrogenase/oxidase (Gene Name=XDH)

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