Structure of PDB 4c5m Chain A Binding Site BS01

Receptor Information
>4c5m Chain A (length=273) 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
YFVVDPVMVCKEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLN
SIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDM
FQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMND
FVGPVDHGAYNRIEHIDVEVTEV
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain4c5m Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4c5m A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		K176 G178 K179 S186 D188 M203 F204 N209 I245
Binding residue
(residue number reindexed from 1)		K173 G175 K176 S183 D185 M200 F201 N206 I242
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K176 N209 G211 A212 G213 C214
Catalytic site (residue number reindexed from 1) K173 N206 G208 A209 G210 C211
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:4c5m, PDBe:4c5m, PDBj:4c5m
PDBsum4c5m
PubMed24601602
UniProtA0A0H3JTP0

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