Structure of PDB 6cfd Chain D Binding Site BS02

Receptor Information
>6cfd Chain D (length=181) Species: 1352 (Enterococcus faecium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPTVIRAYDIYSRLLKDRIIMLSGQVTDDLANSIIAQLLFLDAQDSEKDI
YLYINSPGGSVTAGMAIYDTMNFVKADVQTIVMGMAASMGSFLLTAGTKG
KRFALPNAEIMIHQPLGGAQGQATEIEIAARHILQTRERLNKILAERTGQ
PLEVIEKDTDRDNYMTAEQAKAYGLIDEVME
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 D 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)		R23 D27 I29 Y61 Y63 M93 M190
Binding residue
(residue number reindexed from 1)		R13 D17 I19 Y51 Y53 M83 M180
Annotation score1
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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