Structure of PDB 7dfu Chain F Binding Site BS02

Receptor Information
>7dfu Chain F (length=188) Species: 347 (Xanthomonas oryzae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPMVVEQTSRGERAYDIYSRLLKERLIFLVGPIDDHMANVIVAQLLFLEA
DNPEKDIYIYINSPGGVVTAGMAIYDTMQYIKPDVSTICVGQAASMGALL
LASGAAGKRYALPNSRVMIHQPLGGFQGQATDIDIHAREILTLRSRLNEI
LAKHTGQSLETIARDTERDNFKSAVDAQAYGLVDQVLE
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 chain7dfu Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7dfu Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections.
Resolution1.901 Å
Binding residue
(original residue number in PDB)		E34 Y68 Y70 Y120 L122
Binding residue
(residue number reindexed from 1)		E24 Y58 Y60 Y110 L112
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7dfu, PDBe:7dfu, PDBj:7dfu
PDBsum7dfu
PubMed34218658
UniProtQ5H434|CLPP_XANOR ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

[Back to BioLiP]