Structure of PDB 3hrd Chain A Binding Site BS04

Receptor Information
>3hrd Chain A (length=420) Species: 1528 (Eubacterium barkeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARI
VSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDA
IAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIH
QVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGML
TVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHC
ALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVE
MFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFR
GFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENS
VGLIETLEKAREKAVEVMGY
Ligand information
Ligand IDMCN
InChIInChI=1S/C19H22N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,10-11,17,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H3,21,24,25,26,30)/t5-,6-,10-,11-,17-/m1/s1
InChIKeyRBWYFPNWTRZKKZ-LOIMWUFNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(=C(c4c(nc5c(n4)c(nc(n5)N)O)O3)S)S)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3Oc4nc5nc(N)nc(O)c5nc4C(=C3S)S)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]3C(=C(c4c(nc5c(n4)c(nc(n5)N)O)O3)S)S)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3Oc4nc5nc(N)nc(O)c5nc4C(=C3S)S)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(OCC1Oc2nc3nc(nc(O)c3nc2C(S)=C1S)N)OP(=O)(O)OCC5OC(N4C(=O)N=C(N)C=C4)C(O)C5O
FormulaC19 H22 N8 O13 P2 S2
NamePTERIN CYTOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000263620965
PDB chain3hrd Chain B Residue 921 [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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PDB3hrd The Mo-Se active site of nicotinate dehydrogenase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G237 G238 F239 R351
Binding residue
(residue number reindexed from 1)		G236 G237 F238 R350
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q208 L243 R319 H323 R351
Catalytic site (residue number reindexed from 1) Q207 L242 R318 H322 R350
Enzyme Commision number 1.17.1.5: nicotinate dehydrogenase.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050138 nicotinate dehydrogenase activity
Biological Process
GO:1901848 nicotinate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3hrd, PDBe:3hrd, PDBj:3hrd
PDBsum3hrd
PubMed19549881
UniProtQ0QLF2|NDLMS_EUBBA Nicotinate dehydrogenase large molybdopterin subunit (Gene Name=ndhL)

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