Structure of PDB 3iod Chain B Binding Site BS01

Receptor Information
>3iod Chain B (length=272) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALV
RAAKRVPGSVVVVSIFVNPPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRT
TVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLV
LIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAA
LTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSG
RLLVAARLGTTRLLDNIAIEIG
Ligand information
Ligand IDA6D
InChIInChI=1S/C17H18N6O5S2/c18-15-12-16(20-7-19-15)22(8-21-12)17-14(25)13(24)11(28-17)6-30-29-5-9-2-1-3-10(4-9)23(26)27/h1-4,7-8,11,13-14,17,24-25H,5-6H2,(H2,18,19,20)/t11-,13-,14-,17-/m1/s1
InChIKeyUWYQTICCMFSWOE-LSCFUAHRSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Nc1ncnc2n(cnc12)[CH]3O[CH](CSSCc4cccc(c4)[N+]([O-])=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.0c1cc(cc(c1)[N+](=O)[O-])CSSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O
CACTVS 3.352Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSSCc4cccc(c4)[N+]([O-])=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.0c1cc(cc(c1)[N+](=O)[O-])CSSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
ACDLabs 11.02[O-][N+](=O)c1cccc(c1)CSSCC4OC(n3cnc2c(ncnc23)N)C(O)C4O
FormulaC17 H18 N6 O5 S2
Name(2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol
ChEMBLCHEMBL1230737
DrugBank
ZINCZINC000058638789
PDB chain3iod Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3iod A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry
Resolution1.75 Å
Binding residue
(original residue number in PDB)		P38 T39 M40 G46 H47 L50 F67 N69 V142 F157 G158 K160 D161 Q164 T186 V187 M195
Binding residue
(residue number reindexed from 1)		P37 T38 M39 G45 H46 L49 F66 N68 V126 F141 G142 K144 D145 Q148 T170 V171 M179
Annotation score2
Binding affinityMOAD: Kd=80uM
BindingDB: Kd=80000nM
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 D72 D73 Q76 K144 S180 S181 R182
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:3iod, PDBe:3iod, PDBj:3iod
PDBsum3iod
PubMed19827080
UniProtP9WIL5|PANC_MYCTU Pantothenate synthetase (Gene Name=panC)

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