Structure of PDB 3u7k Chain A Binding Site BS01

Receptor Information
>3u7k Chain A (length=185) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIA
KRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSV
QEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAI
VFQHEIDHLNGVMFYDHIDKDHPLQPHTDAVEVLE
Ligand information
Ligand IDMDB
InChIInChI=1S/C22H34N4O5/c1-22(2,3)19(24-21(29)23-16-11-7-8-12-17(16)31-4)20(28)26(14-18(27)25-30)13-15-9-5-6-10-15/h7-8,11-12,15,19,30H,5-6,9-10,13-14H2,1-4H3,(H,25,27)(H2,23,24,29)/t19-/m1/s1
InChIKeySGGVRJBZDBEGBH-LJQANCHMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1ccccc1OC)NC(C(=O)N(CC(=O)NO)CC2CCCC2)C(C)(C)C
OpenEye OEToolkits 1.7.2CC(C)(C)C(C(=O)N(CC1CCCC1)CC(=O)NO)NC(=O)Nc2ccccc2OC
CACTVS 3.370COc1ccccc1NC(=O)N[CH](C(=O)N(CC2CCCC2)CC(=O)NO)C(C)(C)C
CACTVS 3.370COc1ccccc1NC(=O)N[C@H](C(=O)N(CC2CCCC2)CC(=O)NO)C(C)(C)C
OpenEye OEToolkits 1.7.2CC(C)(C)[C@@H](C(=O)N(CC1CCCC1)CC(=O)NO)NC(=O)Nc2ccccc2OC
FormulaC22 H34 N4 O5
Name(S)-N-(cyclopentylmethyl)-N-(2-(hydroxyamino)-2-oxoethyl)-2-(3-(2-methoxyphenyl)ureido)-3,3-dimethylbutanamide
ChEMBLCHEMBL1209866
DrugBank
ZINCZINC000034047317
PDB chain3u7k Chain A Residue 301 [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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PDB3u7k Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q45 R56 S57 G58 V59 G60 Q65 E109 G110 A111 L112 H154 E155 H158
Binding residue
(residue number reindexed from 1)		Q45 R56 S57 G58 V59 G60 Q65 E109 G110 A111 L112 H154 E155 H158
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.07,Ki=84.9nM
Enzymatic activity
Catalytic site (original residue number in PDB) G60 Q65 C111 L112 H154 E155 H158
Catalytic site (residue number reindexed from 1) G60 Q65 C111 L112 H154 E155 H158
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:0018206 peptidyl-methionine modification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3u7k, PDBe:3u7k, PDBj:3u7k
PDBsum3u7k
PubMed22751663
UniProtQ5HGZ3|DEF_STAAC Peptide deformylase (Gene Name=def)

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