Structure of PDB 3e3u Chain A Binding Site BS01

Receptor Information
>3e3u Chain A (length=196) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVG
LAANQIGCSLRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDT
DDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFARMLQHETG
HLDGFLYLDRLIGRYARNAKRAVKSHGWGVPGLSWLPGEDPDPFGH
Ligand information
Ligand IDNVC
InChIInChI=1S/C19H25N3O4/c1-2-3-7-14(12-21(25)13-23)19(24)22-11-6-9-16(22)18-20-15-8-4-5-10-17(15)26-18/h4-5,8,10,13-14,16,25H,2-3,6-7,9,11-12H2,1H3/t14-,16+/m1/s1
InChIKeyQDDZLTVSNABZIK-ZBFHGGJFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCC[C@H](CN(O)C=O)C(=O)N1CCC[C@H]1c2oc3ccccc3n2
CACTVS 3.341CCCC[CH](CN(O)C=O)C(=O)N1CCC[CH]1c2oc3ccccc3n2
ACDLabs 10.04O=CN(O)CC(C(=O)N3CCCC3c1nc2ccccc2o1)CCCC
OpenEye OEToolkits 1.5.0CCCC[C@H](CN(C=O)O)C(=O)N1CCC[C@H]1c2nc3ccccc3o2
OpenEye OEToolkits 1.5.0CCCCC(CN(C=O)O)C(=O)N1CCCC1c2nc3ccccc3o2
FormulaC19 H25 N3 O4
NameN-[(2R)-2-{[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl}hexyl]-N-hydroxyformamide
ChEMBLCHEMBL506649
DrugBankDB08310
ZINCZINC000040980708
PDB chain3e3u Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3e3u Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results.
Resolution1.56 Å
Binding residue
(original residue number in PDB)		G49 V50 G51 Q56 G105 C106 L107 L141 H148 E149 H152 F195
Binding residue
(residue number reindexed from 1)		G48 V49 G50 Q55 G104 C105 L106 L140 H147 E148 H151 F194
Annotation score1
Binding affinityMOAD: ic50=0.013uM
PDBbind-CN: -logKd/Ki=7.89,IC50=13nM
BindingDB: IC50=13nM
Enzymatic activity
Catalytic site (original residue number in PDB) G51 Q56 C106 L107 H148 E149 H152
Catalytic site (residue number reindexed from 1) G50 Q55 C105 L106 H147 E148 H151
Enzyme Commision number 3.5.1.88: peptide deformylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0042586 peptide deformylase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0043686 co-translational protein modification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3e3u, PDBe:3e3u, PDBj:3e3u
PDBsum3e3u
PubMed19008098
UniProtP9WIJ3|DEF_MYCTU Peptide deformylase (Gene Name=def)

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