Structure of PDB 1dli Chain A Binding Site BS01

Receptor Information
>1dli Chain A (length=402) Species: 1314 (Streptococcus pyogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAVAGSGYVGLSLGVLLSLQNEVTIVDILPSKVDKINNGLSPIQDEYI
EYYLKSKQLSIKATLDSKAAYKEAELVIIATPTNYNSRINYFDTQHVETV
IKEVLSVNSHATLIIKSTIPIGFITEMRQKFQTDRIIFSPEFLRESKALY
DNLYPSRIIVSCEENDSPKVKADAEKFALLLKSAAKKNNVPVLIMGASEA
EAVKLFANTYLALRVAYFNELDTYAESRKLNSHMIIQGISYDDRIGMHYN
NPSFGYGGYCLPKDTKQLLANYNNIPQTLIEAIVSSNNVRKSYIAKQIIN
VLKEQESPVKVVGVYRLIMKSNSDNFRESAIKDVIDILKSKDIKIIIYEP
MLNKLESEDQSVLVNDLENFKKQANIIVTNRYDNELQDVKNKVYSRDIFG
RD
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 chain1dli Chain A Residue 403 [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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PDB1dli The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		G9 Y10 V11 D29 I30 L31 K34 T81 P82 T83 S117 E141 L143 E145 Y259 C260 K263 R327
Binding residue
(residue number reindexed from 1)		G9 Y10 V11 D29 I30 L31 K34 T81 P82 T83 S117 E141 L143 E145 Y259 C260 K263 R327
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T118 E145 K204 N208 C260 D264
Catalytic site (residue number reindexed from 1) T118 E145 K204 N208 C260 D264
Enzyme Commision number 1.1.1.22: UDP-glucose 6-dehydrogenase.
Gene Ontology
Molecular Function
GO:0003979 UDP-glucose 6-dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0000271 polysaccharide biosynthetic process
GO:0006065 UDP-glucuronate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1dli, PDBe:1dli, PDBj:1dli
PDBsum1dli
PubMed10841783
UniProtP0C0F4|UDG_STRPY UDP-glucose 6-dehydrogenase (Gene Name=hasB)

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