Structure of PDB 8sk0 Chain B Binding Site BS01

Receptor Information
>8sk0 Chain B (length=330) Species: 47853 (Micromonospora carbonacea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSVPRVFVAGGAGFIGSHYVRELVAGAYAGWQGCEVTVLDSLTYAG
NLANLAGVRDAVTFVRGDICDGRLLAEVLPGHDVVLNFAAETHVDRSIAD
SAEFLRTNVQGVQSLMQACLTAGVPTIVQVSTDEVYGSIEAGSWSEDAPL
APNSPYAAAKAGGDLIALAYARTYGLPVRITRCGNNYGPYQFPEKVIPLF
LTRLMDGRSVPLYGDGRNVRDWIHVADHCRGIQTVVERGASGEVYHIAGT
AELTNLELTQHLLDAVGGSWDAVERVPDRKGHDRRYSLSDAKLRALGYAP
RVPFADGLAETVAWYRANRHWWEPLRKQLD
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain8sk0 Chain B Residue 502 [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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PDB8sk0 EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster.
Resolution1.51 Å
Binding residue
(original residue number in PDB)		G11 F12 I13 D38 S39 L40 T41 G44 D62 I63 F82 A83 A84 T86 T101 V124 Y150 K154 G178 N180
Binding residue
(residue number reindexed from 1)		G17 F18 I19 D44 S45 L46 T47 G50 D68 I69 F88 A89 A90 T92 T107 V130 Y156 K160 G184 N186
Annotation score1
Enzymatic activity
Enzyme Commision number 4.2.1.46: dTDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008460 dTDP-glucose 4,6-dehydratase activity
GO:0016829 lyase activity
Biological Process
GO:0009225 nucleotide-sugar metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8sk0, PDBe:8sk0, PDBj:8sk0
PDBsum8sk0
PubMed37286037
UniProtA0A1C5ADV9

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