Structure of PDB 8xw9 Chain A Binding Site BS04

Receptor Information
>8xw9 Chain A (length=501) Species: 171101 (Streptococcus pneumoniae R6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNKRVKIVATLGPAVEIRGGKKFGEDGYWGEKLDVEASAKNIAKLIEAGA
NTFRFNFSHGDHQEQGERMATVKLAEKIAGKKVGFLLDTKGPEIRTELFE
GEAKEYSYKTGEKIRVATKQGIKSTREVIALNVAGALDIYDDVEVGRQVL
VDDGKLGLRVVAKDDATREFEVEVENDGIIAKQKGVNIPNTKIPFPALAE
RDNDDIRFGLEQGINFIAISFVRTAKDVNEVRAICEETGNGHVQLFAKIE
NQQGIDNLDEIIEAADGIMIARGDMGIEVPFEMVPVYQKMIIKKVNAAGK
VVITATNMLETMTEKPRATRSEVSDVFNAVIDGTDATMLSGESANGKYPL
ESVTTMATIDKNAQALLNEYGRLDSDSFERNSKTEVMASAVKDATSSMDI
KLVVTLTKTGHTARLISKYRPNADILALTFDELTERGLMLNWGVIPMLTD
APSSTDDMFEIAERKAVEAGLVESGDDIVIVAGVPVGEAVRTNTMRIRTV
R
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain8xw9 Chain A Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8xw9 Structural basis of nucleotide selectivity in pyruvate kinase.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		L11 P13 R54 N56 H59 R95 K184 G341 N345
Binding residue
(residue number reindexed from 1)		L11 P13 R54 N56 H59 R95 K184 G341 N345
Annotation score2
Gene Ontology
Molecular Function
GO:0004743 pyruvate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006096 glycolytic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8xw9, PDBe:8xw9, PDBj:8xw9
PDBsum8xw9
PubMed39009072
UniProtQ8DQ84

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