Structure of PDB 4ddk Chain B Binding Site BS02

Receptor Information
>4ddk Chain B (length=281) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALV
RAAKRVPGSVVVVSIFVNPMQFGAYPRTPDDDLAQLRAEGVEIAFTPTTA
AMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFF
GEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQR
AAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGL
GPMPLNGSGRLLVAARLGTTRLLDNIAIEIG
Ligand information
Ligand ID0HN
InChIInChI=1S/C8H6O4/c9-8(10)5-1-2-6-7(3-5)12-4-11-6/h1-3H,4H2,(H,9,10)
InChIKeyVDVJGIYXDVPQLP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1C(=O)O)OCO2
CACTVS 3.370OC(=O)c1ccc2OCOc2c1
ACDLabs 12.01O=C(O)c1ccc2OCOc2c1
FormulaC8 H6 O4
Name1,3-benzodioxole-5-carboxylic acid;
benzo[d][1,3]dioxole-5-carboxylic acid
ChEMBLCHEMBL573781
DrugBank
ZINCZINC000000158540
PDB chain4ddk Chain B Residue 402 [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]
PDB4ddk Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		R56 P58 R154
Binding residue
(residue number reindexed from 1)		R55 P57 R147
Annotation score1
Binding affinityMOAD: Kd=5.13mM
Enzymatic activity
Catalytic site (original residue number in PDB) M40 H44 H47 D88 D89 Q92 K160 S196 S197 R198
Catalytic site (residue number reindexed from 1) M39 H43 H46 D81 D82 Q85 K153 S189 S190 R191
Enzyme Commision number 6.3.2.1: pantoate--beta-alanine ligase (AMP-forming).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004592 pantoate-beta-alanine ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0015940 pantothenate biosynthetic process
GO:0019482 beta-alanine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ddk, PDBe:4ddk, PDBj:4ddk
PDBsum4ddk
PubMed23872845
UniProtP9WIL5|PANC_MYCTU Pantothenate synthetase (Gene Name=panC)

[Back to BioLiP]