Structure of PDB 6ya4 Chain B Binding Site BS01

Receptor Information
>6ya4 Chain B (length=330) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHHHHHHMSGENLYFQGASAAIVTDTGGVDDKSFNQSAWEGLQAWGKEHN
LSKDNGFTYFQSTSEADYANNLQQAAGSYNLIFGVGFALNNAVKDAAKEH
TDLNYVLIDDVIKDQKNVASVTFADNESGYLAGVAAAKTTKTKQVGFVGG
IESEVISRFEAGFKAGVASVDPSIKVQVDYAGSFGDAAKGKTIAAAQYAA
GADIVYQVAGGTGAGVFAEAKSLNESRPENEKVWVIGVDRDQEAEGKYTS
KDGKESNFVLVSTLKQVGTTVKDISNKAERGEFPGGQVIVYSLKDKGVDL
AVTNLSEEGKKAVEDAKAKILDGSVKVPEK
Ligand information
Ligand IDCTN
InChIInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKeyUHDGCWIWMRVCDJ-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
FormulaC9 H13 N3 O5
Name4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE;
CYTIDINE
ChEMBLCHEMBL95606
DrugBankDB02097
ZINCZINC000002583632
PDB chain6ya4 Chain B Residue 401 [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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PDB6ya4 Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
D28 F37 D112 I159 F187 V211 G213 D242 K268
Binding residue
(residue number reindexed from 1)
D25 F34 D109 I156 F184 V208 G210 D239 K265
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Cellular Component
GO:0005886 plasma membrane

View graph for
Cellular Component
External links
PDB RCSB:6ya4, PDBe:6ya4, PDBj:6ya4
PDBsum6ya4
PubMed33242497
UniProtA0A0H2UPF3

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