Structure of PDB 4de5 Chain A Binding Site BS01

Receptor Information
>4de5 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 ID0JD
InChIInChI=1S/C9H8O4/c10-9(11)8-5-12-6-3-1-2-4-7(6)13-8/h1-4,8H,5H2,(H,10,11)/t8-/m0/s1
InChIKeyHMBHAQMOBKLWRX-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc2c(c1)OC[C@H](O2)C(=O)O
CACTVS 3.370OC(=O)[C@@H]1COc2ccccc2O1
CACTVS 3.370OC(=O)[CH]1COc2ccccc2O1
OpenEye OEToolkits 1.7.6c1ccc2c(c1)OCC(O2)C(=O)O
ACDLabs 12.01O=C(O)C1Oc2ccccc2OC1
FormulaC9 H8 O4
Name(2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000000054811
PDB chain4de5 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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PDB4de5 Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		P38 T39 M40 H47 Q164
Binding residue
(residue number reindexed from 1)		P36 T37 M38 H45 Q162
Annotation score1
Binding affinityMOAD: Kd=670uM
PDBbind-CN: -logKd/Ki=3.15,Kd=0.7mM
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:4de5, PDBe:4de5, PDBj:4de5
PDBsum4de5
PubMed23872845
UniProtP9WIL5|PANC_MYCTU Pantothenate synthetase (Gene Name=panC)

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