Structure of PDB 6yqq Chain A Binding Site BS01

Receptor Information
>6yqq Chain A (length=320) Species: 212423 (Streptomyces kaniharaensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVRVSAPARLSFTLISLDGSSLRRNGIAAMAVDRPGLTAEVREAADGIVA
VTGTAEETARELAAALEALRKLWDGPAARVDVLEALPQHSGFGSKTSTLL
AVGHAYGRLCGVEPDLRELARTLGRGRTSGASTGLSAYGGFLVDGGHVNP
PDFAEAPQKYLVAPPKPVVRLDFPDWPVLVLLTHGRHQEELEWFHSVAPI
PAEESWRTSHLVFMGLAPAVLEQDFDAFCAAVNEITFTGHFKQAQIAFQG
DAVADVLEAGRAAPSVDAIALSVTGPACFAFTKRPEDAERWAWELKNRGL
IRDFWFTRANNQGLATTVVS
Ligand information
Ligand IDPRP
InChIInChI=1S/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1
InChIKeyPQGCEDQWHSBAJP-TXICZTDVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)OP(=O)(O)OP(=O)(O)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)OP(=O)(O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)O[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OC1OC(C(O)C1O)COP(=O)(O)O)(O)OP(=O)(O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)O[P@](O)(=O)O[P](O)(O)=O
FormulaC5 H13 O14 P3
Name1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose;
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;
1-O-pyrophosphono-5-O-phosphono-D-ribose;
1-O-pyrophosphono-5-O-phosphono-ribose
ChEMBL
DrugBankDB01632
ZINCZINC000008215630
PDB chain6yqq 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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PDB6yqq Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		R19 H99 G101 G103 S104 K105 T106 S139 S142
Binding residue
(residue number reindexed from 1)		R9 H89 G91 G93 S94 K95 T96 S129 S132
Annotation score4
Binding affinityMOAD: Kd=4uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016301 kinase activity
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6yqq, PDBe:6yqq, PDBj:6yqq
PDBsum6yqq
PubMed32515440
UniProtA0A5S9CYM0

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