Structure of PDB 4ddk Chain A Binding Site BS01

Receptor Information
>4ddk Chain A (length=289) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVR
AAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAF
TPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRP
DRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYL
DPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLEL
RDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGTFA
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 A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ddk Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H44 G46 L50 G158 P185 T186 V187
Binding residue
(residue number reindexed from 1)		H42 G44 L48 G156 P183 T184 V185
Annotation score1
Binding affinityMOAD: Kd=5.13mM
PDBbind-CN: -logKd/Ki=2.29,Kd=5.1mM
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) M38 H42 H45 D86 D87 Q90 K158 S194 S195 R196
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

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

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