Structure of PDB 3svj Chain P Binding Site BS01

Receptor Information
>3svj Chain P (length=193) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQ
FLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIAYDLEAIMY
NPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHR
IKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE
Ligand information
Ligand ID4LI
InChIInChI=1S/C27H32ClN9O2S/c1-17-7-6-8-18(23(38)29-2)22(17)31-25-32-26(34-27(33-25)37-16-40-15-21(37)24(39)30-3)36-13-11-35(12-14-36)20-10-5-4-9-19(20)28/h4-10,21H,11-16H2,1-3H3,(H,29,38)(H,30,39)(H,31,32,33,34)/t21-/m0/s1
InChIKeyQRGGVLXBPSQEDF-NRFANRHFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1cccc(c1Nc2nc(nc(n2)N3CSCC3C(=O)NC)N4CCN(CC4)c5ccccc5Cl)C(=O)NC
CACTVS 3.370CNC(=O)[CH]1CSCN1c2nc(Nc3c(C)cccc3C(=O)NC)nc(n2)N4CCN(CC4)c5ccccc5Cl
OpenEye OEToolkits 1.7.2Cc1cccc(c1Nc2nc(nc(n2)N3CCN(CC3)c4ccccc4Cl)[N@@]5CSC[C@H]5C(=O)NC)C(=O)NC
ACDLabs 12.01Clc1ccccc1N5CCN(c2nc(nc(n2)N3C(C(=O)NC)CSC3)Nc4c(cccc4C(=O)NC)C)CC5
CACTVS 3.370CNC(=O)[C@@H]1CSCN1c2nc(Nc3c(C)cccc3C(=O)NC)nc(n2)N4CCN(CC4)c5ccccc5Cl
FormulaC27 H32 Cl N9 O2 S
Name(4R)-3-(4-[4-(2-chlorophenyl)piperazin-1-yl]-6-{[2-methyl-6-(methylcarbamoyl)phenyl]amino}-1,3,5-triazin-2-yl)-N-methyl-1,3-thiazolidine-4-carboxamide
ChEMBL
DrugBank
ZINCZINC000089469901
PDB chain3svj Chain P Residue 207 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3svj Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		G69 V71 E126 G127 E128 G129 H173
Binding residue
(residue number reindexed from 1)		G68 V70 E116 G117 E118 G119 H163
Annotation score1
Binding affinityMOAD: Ki=117nM
PDBbind-CN: -logKd/Ki=6.93,Ki=117nM
BindingDB: Ki=117nM
Enzymatic activity
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:3svj, PDBe:3svj, PDBj:3svj
PDBsum3svj
PubMed21711014
UniProtQ8DP79|DEF_STRR6 Peptide deformylase (Gene Name=def)

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