Structure of PDB 1vdv Chain A Binding Site BS05

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 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 chain1vdv 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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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)		E45 G46 L257 V258 V259 G260 N261 T262 E263 I264 F337 A338 A346 S347 G350 N351 I353 T354 S359 D360 I403 L404
Binding residue
(residue number reindexed from 1)		E43 G44 L229 V230 V231 G232 N233 T234 E235 I236 F309 A310 A318 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) 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

View graph for
Molecular Function
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Biological Process
View graph for
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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