Structure of PDB 6afe Chain A Binding Site BS01

Receptor Information
>6afe Chain A (length=187) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVV
ICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGL
IAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGL
ILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLK
Ligand information
Ligand ID72T
InChIInChI=1S/C9H4F3NO2/c10-9(11,12)5-3-1-2-4-6(5)13-8(15)7(4)14/h1-3H,(H,13,14,15)
InChIKeyMXLDJTXXAYVWDF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1cc2c(c(c1)C(F)(F)F)NC(=O)C2=O
CACTVS 3.385FC(F)(F)c1cccc2C(=O)C(=O)Nc12
FormulaC9 H4 F3 N O2
Name7-(trifluoromethyl)-1~{H}-indole-2,3-dione
ChEMBLCHEMBL376435
DrugBank
ZINCZINC000002487385
PDB chain6afe Chain A Residue 201 [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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PDB6afe Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		E18 G75 N76 C106 A107 H126 L128
Binding residue
(residue number reindexed from 1)		E17 G74 N75 C105 A106 H125 L127
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.36,Kd=4.4uM
Enzymatic activity
Enzyme Commision number 3.1.2.-
3.5.1.-
3.5.1.124: protein deglycase.
Gene Ontology
Molecular Function
GO:0001046 core promoter sequence-specific DNA binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003713 transcription coactivator activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005102 signaling receptor binding
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0008233 peptidase activity
GO:0016532 superoxide dismutase copper chaperone activity
GO:0016684 oxidoreductase activity, acting on peroxide as acceptor
GO:0019826 oxygen sensor activity
GO:0019899 enzyme binding
GO:0019900 kinase binding
GO:0019955 cytokine binding
GO:0030414 peptidase inhibitor activity
GO:0030546 signaling receptor activator activity
GO:0036470 tyrosine 3-monooxygenase activator activity
GO:0036478 L-dopa decarboxylase activator activity
GO:0036524 protein deglycase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044388 small protein activating enzyme binding
GO:0044390 ubiquitin-like protein conjugating enzyme binding
GO:0045296 cadherin binding
GO:0045340 mercury ion binding
GO:0050681 nuclear androgen receptor binding
GO:0051920 peroxiredoxin activity
GO:0055105 ubiquitin-protein transferase inhibitor activity
GO:0097110 scaffold protein binding
GO:0140297 DNA-binding transcription factor binding
GO:1903135 cupric ion binding
GO:1903136 cuprous ion binding
GO:1990381 ubiquitin-specific protease binding
GO:1990422 glyoxalase (glycolic acid-forming) activity
Biological Process
GO:0001933 negative regulation of protein phosphorylation
GO:0001963 synaptic transmission, dopaminergic
GO:0002866 positive regulation of acute inflammatory response to antigenic stimulus
GO:0006281 DNA repair
GO:0006508 proteolysis
GO:0006914 autophagy
GO:0006954 inflammatory response
GO:0006979 response to oxidative stress
GO:0007005 mitochondrion organization
GO:0007265 Ras protein signal transduction
GO:0007338 single fertilization
GO:0008344 adult locomotory behavior
GO:0009438 methylglyoxal metabolic process
GO:0010273 detoxification of copper ion
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0019249 lactate biosynthetic process
GO:0019430 removal of superoxide radicals
GO:0030073 insulin secretion
GO:0030091 protein repair
GO:0030521 androgen receptor signaling pathway
GO:0031334 positive regulation of protein-containing complex assembly
GO:0031397 negative regulation of protein ubiquitination
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032679 regulation of TRAIL production
GO:0032757 positive regulation of interleukin-8 production
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0033234 negative regulation of protein sumoylation
GO:0033864 positive regulation of NAD(P)H oxidase activity
GO:0034599 cellular response to oxidative stress
GO:0034614 cellular response to reactive oxygen species
GO:0036471 cellular response to glyoxal
GO:0042177 negative regulation of protein catabolic process
GO:0042542 response to hydrogen peroxide
GO:0042593 glucose homeostasis
GO:0042743 hydrogen peroxide metabolic process
GO:0043523 regulation of neuron apoptotic process
GO:0043524 negative regulation of neuron apoptotic process
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046295 glycolate biosynthetic process
GO:0046826 negative regulation of protein export from nucleus
GO:0050727 regulation of inflammatory response
GO:0050787 detoxification of mercury ion
GO:0050821 protein stabilization
GO:0051583 dopamine uptake involved in synaptic transmission
GO:0051881 regulation of mitochondrial membrane potential
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051899 membrane depolarization
GO:0060081 membrane hyperpolarization
GO:0060765 regulation of androgen receptor signaling pathway
GO:0061691 detoxification of hydrogen peroxide
GO:0061727 methylglyoxal catabolic process to lactate
GO:0070301 cellular response to hydrogen peroxide
GO:0070994 detection of oxidative stress
GO:0106044 guanine deglycation
GO:0106045 guanine deglycation, methylglyoxal removal
GO:0106046 guanine deglycation, glyoxal removal
GO:0110095 cellular detoxification of aldehyde
GO:0140041 cellular detoxification of methylglyoxal
GO:1900182 positive regulation of protein localization to nucleus
GO:1900242 regulation of synaptic vesicle endocytosis
GO:1901984 negative regulation of protein acetylation
GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1902177 positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1902236 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1902903 regulation of supramolecular fiber organization
GO:1902958 positive regulation of mitochondrial electron transport, NADH to ubiquinone
GO:1903073 negative regulation of death-inducing signaling complex assembly
GO:1903094 negative regulation of protein K48-linked deubiquitination
GO:1903122 negative regulation of TRAIL-activated apoptotic signaling pathway
GO:1903181 positive regulation of dopamine biosynthetic process
GO:1903189 glyoxal metabolic process
GO:1903190 glyoxal catabolic process
GO:1903197 positive regulation of L-dopa biosynthetic process
GO:1903376 regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
GO:1903377 negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
GO:1903384 negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway
GO:1903427 negative regulation of reactive oxygen species biosynthetic process
GO:1903428 positive regulation of reactive oxygen species biosynthetic process
GO:1903599 positive regulation of autophagy of mitochondrion
GO:1903751 negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide
GO:1905259 negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway
GO:2000277 positive regulation of oxidative phosphorylation uncoupler activity
GO:2000379 positive regulation of reactive oxygen species metabolic process
GO:2001237 negative regulation of extrinsic apoptotic signaling pathway
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005759 mitochondrial matrix
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005912 adherens junction
GO:0008021 synaptic vesicle
GO:0016605 PML body
GO:0030424 axon
GO:0043005 neuron projection
GO:0044297 cell body
GO:0045121 membrane raft
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6afe, PDBe:6afe, PDBj:6afe
PDBsum6afe
PubMed30063823
UniProtQ99497|PARK7_HUMAN Parkinson disease protein 7 (Gene Name=PARK7)

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