Structure of PDB 6ow2 Chain P Binding Site BS01

Receptor Information
>6ow2 Chain P (length=191) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQ
FLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNAYDLEAIMYN
PKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRI
KLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLIL
Ligand information
Ligand IDNB4
InChIInChI=1S/C22H36FN7O4/c1-15-24-20(19(23)21(25-15)29-7-6-28-8-9-34-13-18(28)12-29)26-27-22(32)17(11-30(33)14-31)10-16-4-2-3-5-16/h16-18,31,33H,2-14H2,1H3,(H,27,32)(H,24,25,26)/t17-,18+/m1/s1
InChIKeyZUQCOBLJLUYLKK-MSOLQXFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1nc(c(c(n1)N2CCN3CCOCC3C2)F)NNC(=O)C(CC4CCCC4)CN(CO)O
CACTVS 3.385Cc1nc(NNC(=O)[CH](CC2CCCC2)CN(O)CO)c(F)c(n1)N3CCN4CCOC[CH]4C3
ACDLabs 12.01C(C1CCCC1)C(C(NNc2nc(C)nc(c2F)N4CCN3CCOCC3C4)=O)CN(CO)O
OpenEye OEToolkits 2.0.7Cc1nc(c(c(n1)N2CCN3CCOC[C@@H]3C2)F)NNC(=O)[C@H](CC4CCCC4)CN(CO)O
CACTVS 3.385Cc1nc(NNC(=O)[C@H](CC2CCCC2)CN(O)CO)c(F)c(n1)N3CCN4CCOC[C@@H]4C3
FormulaC22 H36 F N7 O4
Name(2R)-2-(cyclopentylmethyl)-N'-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide
ChEMBL
DrugBank
ZINC
PDB chain6ow2 Chain P Residue 302 [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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PDB6ow2 Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q57 G69 G70 V71 G72 Q77 E128 C130 L131 V170 H173 E174 H177
Binding residue
(residue number reindexed from 1)		Q56 G68 G69 V70 G71 Q76 E117 C119 L120 V159 H162 E163 H166
Annotation score1
Binding affinityMOAD: ic50=3nM
PDBbind-CN: -logKd/Ki=8.52,IC50=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) G72 Q77 C130 L131 H173 E174 H177
Catalytic site (residue number reindexed from 1) G71 Q76 C119 L120 H162 E163 H166
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:6ow2, PDBe:6ow2, PDBj:6ow2
PDBsum6ow2
PubMed31160176
UniProtQ8DP79|DEF_STRR6 Peptide deformylase (Gene Name=def)

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