Structure of PDB 3bdj Chain A Binding Site BS06

Receptor Information
>3bdj Chain A (length=1286) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADELVFFVNGKKVVEKNADPETTLLAYLRRKLGLRGTKLGCGEGGCGACT
VMLSKYDRLQDKIIHFSANACLAPICTLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTVEEIEDAFQGNLCRCTG
YRPILQGFRTFAPSLFNPEEFMPLDPTQEPIFPPELLRLKDVPPKQLRFE
GERVTWIQASTLKELLDLKAQHPEAKLVVGNTEIGIEMKFKNQLFPMIIC
PAWIPELNAVEHGPEGISFGAACALSSVEKTLLEAVAKLPTQKTEVFRGV
LEQLRWFAGKQVKSVASLGGNIITASPISDLNPVFMASGTKLTIVSRGTR
RTVPMDHTFFPSYRKTLLGPEEILLSIEIPYSREDEFFSAFKQASRREDD
IAKVTCGMRVLFQPGSMQVKELALCYGGMADRTISALKTTQKQLSKFWNE
KLLQDVCAGLAEELSLSPDAPGGMIEFRRTLTLSFFFKFYLTVLKKLGKL
DPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAAMQASG
EAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVCFLSAD
DIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAHVVKVT
YEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGELYIGG
QDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVPVNRIL
VRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDMLITGG
RHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALFHMDNC
YKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVTCGLPA
EEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSEVDKFN
KENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSHGGTEM
GQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVSTDIYGQ
AVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFYRTPNL
GYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNP
AIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPTE
FRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARAQHTNN
NTKELFRLDSPATPEKIRNACVDKFTTLCKPWSLRV
Ligand information
Ligand ID141
InChIInChI=1S/C5H4N4O2/c10-4-2-1-6-9-3(2)7-5(11)8-4/h1H,(H3,6,7,8,9,10,11)
InChIKeyHXNFUBHNUDHIGC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1N=C2C(C(=O)N1)=CNN2
OpenEye OEToolkits 1.7.6C1=C2C(=NC(=O)NC2=O)NN1
CACTVS 3.385O=C1NC(=O)C2=CNNC2=N1
FormulaC5 H4 N4 O2
NameOxypurinol;
Alloxanthine
ChEMBLCHEMBL859
DrugBankDB05262
ZINCZINC000084462581
PDB chain3bdj Chain A Residue 5101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3bdj Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E802 R880 F914 F1009 T1010 A1078 A1079 E1261
Binding residue
(residue number reindexed from 1)		E764 R842 F876 F971 T972 A1040 A1041 E1223
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q767 E802 R880 H884 R912 G1260 E1261
Catalytic site (residue number reindexed from 1) Q729 E764 R842 H846 R874 G1222 E1223
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:3bdj, PDBe:3bdj, PDBj:3bdj
PDBsum3bdj
PubMed18600558
UniProtP80457|XDH_BOVIN Xanthine dehydrogenase/oxidase (Gene Name=XDH)

[Back to BioLiP]