Structure of PDB 3ioc Chain A Binding Site BS01

Receptor Information

>3ioc Chain A (length=273) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRA
AKRVPGSVVVVSIFVNPMQTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLR
TTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQL
VLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSA
ALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGS
GRLLVAARLGTTRLLDNIAIEIG

Ligand information

Ligand ID

A5D

InChI

InChI=1S/C17H19N5O3S2/c18-15-12-16(20-8-19-15)22(9-21-12)17-14(24)13(23)11(25-17)7-27-26-6-10-4-2-1-3-5-10/h1-5,8-9,11,13-14,17,23-24H,6-7H2,(H2,18,19,20)/t11-,13-,14-,17-/m1/s1

InChIKey

DBQUNXDCOIKHGM-LSCFUAHRSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	c1ccc(cc1)CSSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
OpenEye OEToolkits 1.7.0	c1ccc(cc1)CSSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O
CACTVS 3.352	Nc1ncnc2n(cnc12)[CH]3O[CH](CSSCc4ccccc4)[CH](O)[CH]3O
CACTVS 3.352	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSSCc4ccccc4)[C@@H](O)[C@H]3O
ACDLabs 11.02	n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSSCc4ccccc4)N

Formula

C17 H19 N5 O3 S2

Name

(2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-[(benzyldisulfanyl)methyl]tetrahydrofuran-3,4-diol

PDB chain

3ioc Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3ioc A Fragment-Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry
Resolution	2.5 Å
Binding residue (original residue number in PDB)	P38 H44 G46 H47 L50 V142 F157 G158 K160 D161 Q164 T186 V187 M195
Binding residue (residue number reindexed from 1)	P35 H41 G43 H44 L47 V127 F142 G143 K145 D146 Q149 T171 V172 M180
Annotation score	2
Binding affinity	MOAD: Kd=210uM PDBbind-CN: -logKd/Ki=3.68,Kd=210uM BindingDB: Kd=210000nM

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 D73 D74 Q77 K145 S181 S182 R183
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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Cellular Component

External links

PDB	RCSB:3ioc, PDBe:3ioc, PDBj:3ioc
PDBsum	3ioc
PubMed	19827080
UniProt	P9WIL5\|PANC_MYCTU Pantothenate synthetase (Gene Name=panC)

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