Structure of PDB 4c5k Chain D Binding Site BS01

Receptor Information
>4c5k Chain D (length=276) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWS
HDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQ
YFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLG
KLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLT
TDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWK
MNDFVGPVDHGAYNRIEHIDVEVTEV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4c5k Chain D Residue 1277 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4c5k A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		K176 G178 K179 S186 D188 M203 F204 N209 I245
Binding residue
(residue number reindexed from 1)		K176 G178 K179 S186 D188 M203 F204 N209 I245
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K176 N209 G211 A212 G213 C214
Catalytic site (residue number reindexed from 1) K176 N209 G211 A212 G213 C214
Enzyme Commision number 2.7.1.35: pyridoxal kinase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008902 hydroxymethylpyrimidine kinase activity
GO:0008972 phosphomethylpyrimidine kinase activity
GO:0016301 kinase activity
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0016310 phosphorylation
Cellular Component
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:4c5k, PDBe:4c5k, PDBj:4c5k
PDBsum4c5k
PubMed24601602
UniProtA0A0H3JTP0

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