Structure of PDB 1r6d Chain A Binding Site BS01

Receptor Information
>1r6d Chain A (length=322) Species: 54571 (Streptomyces venezuelae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRLLVTGGAGFIGSHFVRQLLAGAYPDVPADEVIVLDSLTYAGNRANLAP
VDADPRLRFVHGDIRDAGLLARELRGVDAIVHFAAESHVDRSIAGASVFT
ETNVQGTQTLLQCAVDAGVGRVVHVSTNQVYGSIDSGSWTESSPLEPNSP
YAASKAGSDLVARAYHRTYGLDVRITRCCNNYGPYQHPEKLIPLFVTNLL
DGGTLPLYGDGANVREWVHTDDHCRGIALVLAGGRAGEIYHIGGGLELTN
RELTGILLDSLGADWSSVRKVADRKGHDLRYSLDGGKIERELGYRPQVSF
ADGLARTVRWYRENRGWWEPLK
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 chain1r6d Chain A Residue 400 [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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PDB1r6d High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae
Resolution1.35 Å
Binding residue
(original residue number in PDB)		G10 F11 I12 D37 S38 L39 T40 A42 G43 D63 I64 F83 A84 A85 S87 T102 V125 S126 Y151 K155 N181
Binding residue
(residue number reindexed from 1)		G10 F11 I12 D37 S38 L39 T40 A42 G43 D63 I64 F83 A84 A85 S87 T102 V125 S126 Y151 K155 N181
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T127 N128 Q129 Y151 K155
Catalytic site (residue number reindexed from 1) T127 N128 Q129 Y151 K155
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:0016491 oxidoreductase 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:1r6d, PDBe:1r6d, PDBj:1r6d
PDBsum1r6d
PubMed14570895
UniProtQ9ZGH3

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