Structure of PDB 6cfd Chain B Binding Site BS01

Receptor Information
>6cfd Chain B (length=182) Species: 1352 (Enterococcus faecium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPTVIERAYDIYSRLLKDRIIMLSGQVTDDLANSIIAQLLFLDAQDSEKD
IYLYINSPGGSVTAGMAIYDTMNFVKADVQTIVMGMAASMGSFLLTAGTK
GKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILQTRERLNKILAERTG
QPLEVIEKDTDRDNYMTAEQAKAYGLIDEVME
Ligand information
Ligand IDEZA
InChIInChI=1S/C39H52F2N6O8/c1-4-5-6-7-13-33(48)43-28(19-25-17-26(40)20-27(41)18-25)34(49)44-29-22-55-39(54)32-16-23(2)21-47(32)36(51)24(3)42-35(50)30-11-8-9-14-45(30)38(53)31-12-10-15-46(31)37(29)52/h7,13,17-18,20,23-24,28-32H,4-6,8-12,14-16,19,21-22H2,1-3H3,(H,42,50)(H,43,48)(H,44,49)/b13-7+/t23-,24-,28+,29+,30+,31+,32+/m1/s1
InChIKeyBAEUBYUDIYWBPI-AIRHAPKHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCC=CC(=O)NC(Cc1cc(cc(c1)F)F)C(=O)NC2COC(=O)C3CC(CN3C(=O)C(NC(=O)C4CCCCN4C(=O)C5CCCN5C2=O)C)C
CACTVS 3.385CCCC\C=C\C(=O)N[C@@H](Cc1cc(F)cc(F)c1)C(=O)N[C@H]2COC(=O)[C@@H]3C[C@@H](C)CN3C(=O)[C@@H](C)NC(=O)[C@@H]4CCCCN4C(=O)[C@@H]5CCCN5C2=O
ACDLabs 12.01C(Cc1cc(F)cc(c1)F)(C(=O)NC2C(N5C(C(N4C(C(NC(C(N3C(C(OC2)=O)CC(C3)C)=O)C)=O)CCCC4)=O)CCC5)=O)NC(C=[C@H]CCCC)=O
OpenEye OEToolkits 2.0.6CCCC/C=C/C(=O)N[C@@H](Cc1cc(cc(c1)F)F)C(=O)N[C@H]2COC(=O)[C@@H]3C[C@H](CN3C(=O)C(NC(=O)[C@@H]4CCCCN4C(=O)[C@@H]5CCCN5C2=O)C)C
CACTVS 3.385CCCCC=CC(=O)N[CH](Cc1cc(F)cc(F)c1)C(=O)N[CH]2COC(=O)[CH]3C[CH](C)CN3C(=O)[CH](C)NC(=O)[CH]4CCCCN4C(=O)[CH]5CCCN5C2=O
FormulaC39 H52 F2 N6 O8
Name
ChEMBL
DrugBank
ZINC
PDB chain6cfd Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6cfd In VivoandIn VitroEffects of a ClpP-Activating Antibiotic against Vancomycin-Resistant Enterococci.
Resolution2.57 Å
Binding residue
(original residue number in PDB)		L49 T80 F83
Binding residue
(residue number reindexed from 1)		L40 T71 F74
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.86,Kd=13.9nM
Enzymatic activity
Enzyme Commision number 3.4.21.92: endopeptidase Clp.
Gene Ontology
Molecular Function
GO:0004176 ATP-dependent peptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0051117 ATPase binding
Biological Process
GO:0006508 proteolysis
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
Cellular Component
GO:0005737 cytoplasm
GO:0009368 endopeptidase Clp complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6cfd, PDBe:6cfd, PDBj:6cfd
PDBsum6cfd
PubMed29784838
UniProtQ3XX76

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