Structure of PDB 7zzo Chain B Binding Site BS03

Receptor Information
>7zzo Chain B (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHK
ATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFE
FCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVL
AILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGT
GDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVV
LQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNV
ARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEY
MEKIKQRLFENLRMLP
Ligand information
Ligand IDKIZ
InChIInChI=1S/C11H15FN2O/c1-14(2)11(15)10(13)7-8-3-5-9(12)6-4-8/h3-6,10H,7,13H2,1-2H3/p+1/t10-/m1/s1
InChIKeySLKQPFCNEFCUMC-SNVBAGLBSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN(C)C(=O)[C@@H](Cc1ccc(cc1)F)[NH3+]
CACTVS 3.385CN(C)C(=O)[CH]([NH3+])Cc1ccc(F)cc1
CACTVS 3.385CN(C)C(=O)[C@H]([NH3+])Cc1ccc(F)cc1
OpenEye OEToolkits 2.0.7CN(C)C(=O)C(Cc1ccc(cc1)F)[NH3+]
FormulaC11 H16 F N2 O
Name[(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium
ChEMBL
DrugBank
ZINC
PDB chain7zzo Chain B Residue 606 [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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PDB7zzo Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		M35 L144 H145 H146 G154 F155 C156 D181 H183 F210 D269 G305 G306 Y308
Binding residue
(residue number reindexed from 1)		M22 L131 H132 H133 G141 F142 C143 D168 H170 F197 D256 G292 G293 Y295
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0019899 enzyme binding
GO:0031072 heat shock protein binding
GO:0031492 nucleosomal DNA binding
GO:0033558 protein lysine deacetylase activity
GO:0042393 histone binding
GO:0042826 histone deacetylase binding
GO:0051059 NF-kappaB binding
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
GO:0160010 protein de-2-hydroxyisobutyrylase activity
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001975 response to amphetamine
GO:0003300 cardiac muscle hypertrophy
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0008284 positive regulation of cell population proliferation
GO:0009410 response to xenobiotic stimulus
GO:0009913 epidermal cell differentiation
GO:0010718 positive regulation of epithelial to mesenchymal transition
GO:0010944 negative regulation of transcription by competitive promoter binding
GO:0010977 negative regulation of neuron projection development
GO:0016358 dendrite development
GO:0030336 negative regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0031000 response to caffeine
GO:0031507 heterochromatin formation
GO:0032496 response to lipopolysaccharide
GO:0032732 positive regulation of interleukin-1 production
GO:0032760 positive regulation of tumor necrosis factor production
GO:0032922 circadian regulation of gene expression
GO:0032967 positive regulation of collagen biosynthetic process
GO:0034605 cellular response to heat
GO:0035094 response to nicotine
GO:0036211 protein modification process
GO:0042220 response to cocaine
GO:0042475 odontogenesis of dentin-containing tooth
GO:0042659 regulation of cell fate specification
GO:0042733 embryonic digit morphogenesis
GO:0043066 negative regulation of apoptotic process
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0045347 negative regulation of MHC class II biosynthetic process
GO:0045862 positive regulation of proteolysis
GO:0045892 negative regulation of DNA-templated transcription
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048149 behavioral response to ethanol
GO:0048511 rhythmic process
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0055093 response to hyperoxia
GO:0060789 hair follicle placode formation
GO:0061000 negative regulation of dendritic spine development
GO:0061029 eyelid development in camera-type eye
GO:0061198 fungiform papilla formation
GO:0070301 cellular response to hydrogen peroxide
GO:0071300 cellular response to retinoic acid
GO:0071560 cellular response to transforming growth factor beta stimulus
GO:0097305 response to alcohol
GO:1902437 positive regulation of male mating behavior
GO:1902455 negative regulation of stem cell population maintenance
GO:1902459 positive regulation of stem cell population maintenance
GO:1903351 cellular response to dopamine
GO:1904645 response to amyloid-beta
GO:2000273 positive regulation of signaling receptor activity
GO:2000736 regulation of stem cell differentiation
GO:2000757 negative regulation of peptidyl-lysine acetylation
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016581 NuRD complex
GO:0032991 protein-containing complex
GO:0035098 ESC/E(Z) complex
GO:0070822 Sin3-type complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7zzo, PDBe:7zzo, PDBj:7zzo
PDBsum7zzo
PubMed36262388
UniProtQ92769|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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