Structure of PDB 3iod Chain A Binding Site BS01

Receptor Information
>3iod Chain A (length=276) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRA
AKRVPGSVVVVSIFVNPMQFLDAYPRTPDDDLAQLRAEGVEIAFTPTTAA
MYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFG
EKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRA
AAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLG
NGSGRLLVAARLGTTRLLDNIAIEIG
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 A Residue 302 [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 H44 G46 H47 F67 Q72 F157 G158 D161 Q164 T186 V187 M195
Binding residue
(residue number reindexed from 1)		P35 T36 M37 H41 G43 H44 F64 Q69 F149 G150 D153 Q156 T178 V179 M187
Annotation score2
Binding affinityMOAD: Kd=80uM
PDBbind-CN: -logKd/Ki=4.10,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) M37 H41 H44 D80 D81 Q84 K152 S188 S189 R190
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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