Structure of PDB 6ow7 Chain Q Binding Site BS01

Receptor Information
>6ow7 Chain Q (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 IDN9Y
InChIInChI=1S/C20H29N5O4/c26-14-24(29)13-16(12-15-6-1-2-7-15)20(28)25-17(8-5-11-22-25)19(27)23-18-9-3-4-10-21-18/h3-4,9-10,14-17,22,29H,1-2,5-8,11-13H2,(H,21,23,27)/t16-,17+/m1/s1
InChIKeyIGYIJLMSSQSKHF-SJORKVTESA-N
SMILES
SoftwareSMILES
CACTVS 3.385ON(C[CH](CC1CCCC1)C(=O)N2NCCC[CH]2C(=O)Nc3ccccn3)C=O
OpenEye OEToolkits 2.0.7c1ccnc(c1)NC(=O)C2CCCNN2C(=O)C(CC3CCCC3)CN(C=O)O
OpenEye OEToolkits 2.0.7c1ccnc(c1)NC(=O)[C@@H]2CCCNN2C(=O)[C@H](CC3CCCC3)CN(C=O)O
CACTVS 3.385ON(C[C@@H](CC1CCCC1)C(=O)N2NCCC[C@H]2C(=O)Nc3ccccn3)C=O
ACDLabs 12.01C(N(C=O)O)C(CC1CCCC1)C(N2C(CCCN2)C(=O)Nc3ccccn3)=O
FormulaC20 H29 N5 O4
Name(3S)-2-{(2R)-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanoyl}-N-(pyridin-2-yl)hexahydropyridazine-3-carboxamide
ChEMBLCHEMBL4466084
DrugBank
ZINC
PDB chain6ow7 Chain Q Residue 303 [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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PDB6ow7 Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		R68 G69 G70 V71 G72 Q77 G129 C130 L131 H173 E174 H177
Binding residue
(residue number reindexed from 1)		R67 G68 G69 V70 G71 Q76 G118 C119 L120 H162 E163 H166
Annotation score1
Binding affinityMOAD: ic50=1nM
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:6ow7, PDBe:6ow7, PDBj:6ow7
PDBsum6ow7
PubMed31160176
UniProtQ8DP79|DEF_STRR6 Peptide deformylase (Gene Name=def)

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