Structure of PDB 3hrd Chain B Binding Site BS01

Receptor Information
>3hrd Chain B (length=330) Species: 1528 (Eubacterium barkeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKKRGKGVGSMWYGIGNTGLPNPAAAFVEIHGDGSANVMFGAADIGQGSG
TAMAQIAAEELGLDYEKIHVTWGDTMVTPDGGATSASRQTLITGNAVILA
CRQAKETLAKTAAEKLDCAPEELSFRDNTVFITADPERSMTYGELMAAMK
AAGRMAVGAGSYNPNTTGLAPENMSGIPFEVYSYATTIAEVEVDTETGEV
DVLKVVSAHDVGTPINRSMVEGQIEGGVTMGQGFVLMEEIEVNTKNGAIK
NPSMSKYIIPSNRDVPEIHSILVESEGGPGPFGAKGVGEPALIPMIPAVV
AAIEDALGTRFTHTPIMPKDIVAAVKAQEK
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)		I45 G46 Q47 G48 S49 S85 S87 Q89 T90 I215 N216 M219 V220 Q223 K285 G286 V287 G288 E289
Binding residue
(residue number reindexed from 1)		I45 G46 Q47 G48 S49 S85 S87 Q89 T90 I215 N216 M219 V220 Q223 K285 G286 V287 G288 E289
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E289 P290
Catalytic site (residue number reindexed from 1) E289 P290
Enzyme Commision number 1.17.1.5: nicotinate dehydrogenase.
Gene Ontology
Molecular Function
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
UniProtQ0QLF1|NDMMS_EUBBA Nicotinate dehydrogenase medium molybdopterin subunit (Gene Name=ndhM)

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