Structure of PDB 1vdv Chain A Binding Site BS06

Receptor Information
>1vdv Chain A (length=1299) 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
KDSKLDPTYTSATLLFQKHPPANIQLFQEVPNGQSKEDTVGRPLPHLAAA
MQASGEAVYCDDIPRYENELFLRLVTSTRAHAKIKSIDVSEAQKVPGFVC
FLSADDIPGSNETGLFNDETVFAKDTVTCVGHIIGAVVADTPEHAERAAH
VVKVTYEDLPAIITIEDAIKNNSFYGSELKIEKGDLKKGFSEADNVVSGE
LYIGGQDHFYLETHCTIAIPKGEEGEMELFVSTQNAMKTQSFVAKMLGVP
VNRILVRVKRMGGGFGGKETRSTLVSVAVALAAYKTGHPVRCMLDRNEDM
LITGGRHPFLARYKVGFMKTGTIVALEVDHYSNAGNSRDLSHSIMERALF
HMDNCYKIPNIRGTGRLCKTNLSSNTAFRGFGGPQALFIAENWMSEVAVT
CGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYARKSE
VDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALIHVYTDGSVLVSH
GGTEMGQGLHTKMVQVASKALKIPISKIYISETSTNTVPNSSPTAASVST
DIYGQAVYEACQTILKRLEPFKKKNPDGSWEDWVMAAYQDRVSLSTTGFY
RTPNLGYSFETNSGNAFHYFTYGVACSEVEIDCLTGDHKNLRTDIVMDVG
SSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFG
SIPTEFRVSLLRDCPNKKAIYASKAVGEPPLFLGASVFFAIKDAIRAARA
QHTNNNTKELFRLDSPATPEKIRNACVDKFTTLCVTGAPGNCKPWSLRV
Ligand information
Ligand IDYSH
InChIInChI=1S/C16H17N3O3/c1-16(2,3)10-22-14-5-4-13(6-11(14)7-17)19-9-12(8-18-19)15(20)21/h4-6,8-9H,10H2,1-3H3,(H,20,21)
InChIKeyAETHRPHBGJAIBT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(C)COc1ccc(cc1C#N)n2cc(cn2)C(=O)O
CACTVS 3.341CC(C)(C)COc1ccc(cc1C#N)n2cc(cn2)C(O)=O
ACDLabs 10.04N#Cc1c(OCC(C)(C)C)ccc(c1)n2ncc(c2)C(=O)O
FormulaC16 H17 N3 O3
Name1-[3-CYANO-4-(NEOPENTYLOXY)PHENYL]-1H-PYRAZOLE-4-CARBOXYLIC ACID;
Y-700
ChEMBLCHEMBL169526
DrugBankDB03841
ZINCZINC000000007343
PDB chain1vdv 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

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PDB1vdv Y-700 [1-[3-Cyano-4-(2,2-dimethylpropoxy)phenyl]-1H-pyrazole-4-carboxylic acid]: a potent xanthine oxidoreductase inhibitor with hepatic excretion
Resolution1.98 Å
Binding residue
(original residue number in PDB)		E802 L873 S876 R880 F914 F1009 T1010 V1011 L1014 P1076 A1079
Binding residue
(residue number reindexed from 1)		E769 L840 S843 R847 F881 F976 T977 V978 L981 P1043 A1046
Annotation score1
Binding affinityBindingDB: IC50=5.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q767 E802 R880 H884 R912 G1260 E1261
Catalytic site (residue number reindexed from 1) Q734 E769 R847 H851 R879 G1227 E1228
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1vdv, PDBe:1vdv, PDBj:1vdv
PDBsum1vdv
PubMed15190124
UniProtP80457|XDH_BOVIN Xanthine dehydrogenase/oxidase (Gene Name=XDH)

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