Structure of PDB 2i5b Chain D Binding Site BS01

Receptor Information
>2i5b Chain D (length=267) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMHKALTIAGSDSSGGAGIQADLKTFQEKNVYGMTALTVIVAMDPNNSWN
HQVFPIDTDTIRAQLATITDGIGVDAMKTGMLPTVDIIELAAKTIKEKQL
KNVVIDPVMVCKGANEVLYPEHAQALREQLAPLATVITPNLFEASQLSGM
DELKTVDDMIEAAKKIHALGAQYVVITGGGKLKHEKAVDVLYDGETAEVL
ESEMIDTPYTHGAGCTFSAAVTAELAKGAEVKEAIYAAKEFITAAIKESF
PLNQYVGPTKHSALRLN
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 chain2i5b Chain D Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2i5b The Crystal Structure of an ADP Complex of Bacillus subtilis Pyridoxal Kinase Provides Evidence for the Parallel Emergence of Enzyme Activity During Evolution.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		N141 T178 G180 G181 K182 A188 D190 I206 G215 I247
Binding residue
(residue number reindexed from 1)		N140 T177 G179 G180 K181 A187 D189 I205 G214 I246
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T178 T211 G213 A214 G215 C216
Catalytic site (residue number reindexed from 1) T177 T210 G212 A213 G214 C215
Enzyme Commision number 2.7.1.35: pyridoxal kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008478 pyridoxal kinase activity
GO:0008902 hydroxymethylpyrimidine kinase activity
GO:0008972 phosphomethylpyrimidine kinase activity
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0009228 thiamine biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2i5b, PDBe:2i5b, PDBj:2i5b
PDBsum2i5b
PubMed16978644
UniProtP39610|PDXK_BACSU Pyridoxine kinase (Gene Name=pdxK)

[Back to BioLiP]