Structure of PDB 2ckj Chain A Binding Site BS03

Receptor Information
>2ckj Chain A (length=1264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLSGTKLGCGEGGCGACT
VMLSKYDRLQNKIVHFSANACLAPICSLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTMEEIENAFQGNLCRCTG
YRPILQGFRTFARPSLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQLRF
EGERVTWIQASTLKELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPMIV
CPAWIPELNSVEHGPDGISFGAACPLSIVEKTLVDAVAKLPAQKTEVFRG
VLEQLRWFAGKQVKSVASVGGNIITASPISDLNPVFMASGAKLTLVSRGT
RRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSREGEYFSAFKQASDIAK
VTSGMRVLFKPGTTEVQELALCYGGMANRTISALKTTQRQLSKLWKEELL
QDVCAGLAEELHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLGQENLE
VQLFQEVPKGQSEEDMVGRPLPHLAADMQASGEAVYCDDIPRYENELSLR
LVTSTRAHAKIKSIDTSEAKKVPGFVCFISADDVPGSNITGICNDETVFA
KDKVTCVGHIIGAVVADTPEHTQRAAQGVKITYEELPAIITIEDAIKNNS
FYGPELKIEKGDLKKGFSEADNVVSGEIYIGGQEHFYLETHCTIAVPKGE
AGEMELFVSTQNTMKTQSFVAKMLGVPANRIVVRVKRMGGGFGGKETRST
VVSTAVALAAYKTGRPVRCMLDRDEDMLITGGRHPFLARYKVGFMKTGTV
VALEVDHFSNVGNTQDLSQSIMERALFHMDNCYKIPNIRGTGRLCKTNLP
SNTAFRGFGGPQGMLIAECWMSEVAVTCGMPAEEVRRKNLYKEGDLTHFN
QKLEGFTLPRCWEECLASSQYHARKSEVDKFNKENCWKKRGLCIIPTKFG
ISFTVPFLNQAGALLHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKI
PTSKIYISETSTNTVPNTSPTAASVSADLNGQAVYAACQTILKRLEPYKK
KNPSGSWEDWVTAAYMDTVSLSATGFYRTPNLGYSFETNSGNPFHYFSYG
VACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLF
TLEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKKAIYAS
KAVGEPPLFLAASIFFAIKDAIRAARAQHTGNNVKELFRLDSPATPEKIR
NACVDKFTTLCVTW
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 chain2ckj Chain A Residue 3006 [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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PDB2ckj Human Milk Xanthine Dehydrogenase is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation.
Resolution3.59 Å
Binding residue
(original residue number in PDB)		L257 V259 G260 N261 T262 E263 F337 A338 A346 S347 G350 N351 I353 T354 D360 L404
Binding residue
(residue number reindexed from 1)		L228 V230 G231 N232 T233 E234 F308 A309 A317 S318 G321 N322 I324 T325 D331 L375
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Q768 E803 R881 H885 R913 G1261 E1262
Catalytic site (residue number reindexed from 1) Q711 E746 R824 H828 R856 G1204 E1205
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:0005515 protein binding
GO:0016491 oxidoreductase activity
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:0070674 hypoxanthine dehydrogenase activity
GO:0070675 hypoxanthine oxidase activity
GO:0071949 FAD binding
Biological Process
GO:0000255 allantoin metabolic process
GO:0001933 negative regulation of protein phosphorylation
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:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0007595 lactation
GO:0009114 hypoxanthine catabolic process
GO:0009115 xanthine catabolic process
GO:0010629 negative regulation of gene expression
GO:0016226 iron-sulfur cluster assembly
GO:0030856 regulation of epithelial cell differentiation
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: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:2ckj, PDBe:2ckj, PDBj:2ckj
PDBsum2ckj
PubMed
UniProtP47989|XDH_HUMAN Xanthine dehydrogenase/oxidase (Gene Name=XDH)

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