Structure of PDB 7zzt Chain B Binding Site BS03

Receptor Information

>7zzt 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 ID

KJF

InChI

InChI=1S/C14H20N2O/c15-13(14(17)16-10-4-5-11-16)9-8-12-6-2-1-3-7-12/h1-3,6-7,13H,4-5,8-11,15H2/p+1/t13-/m1/s1

InChIKey

WCADMWMQCHZJOA-CYBMUJFWSA-O

SMILES

Software	SMILES
CACTVS 3.385	[NH3+][CH](CCc1ccccc1)C(=O)N2CCCC2
CACTVS 3.385	[NH3+][C@H](CCc1ccccc1)C(=O)N2CCCC2
OpenEye OEToolkits 3.1.0.0	c1ccc(cc1)CC[C@H](C(=O)N2CCCC2)[NH3+]
OpenEye OEToolkits 3.1.0.0	c1ccc(cc1)CCC(C(=O)N2CCCC2)[NH3+]

Formula

C14 H21 N2 O

Name

[(2~{R})-1-oxidanylidene-4-phenyl-1-pyrrolidin-1-yl-butan-2-yl]azanium

ChEMBL

DrugBank

ZINC

PDB chain

7zzt Chain B Residue 610 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7zzt Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.
Resolution	1.56 Å
Binding residue (original residue number in PDB)	M35 L144 H146 G154 F155 C156 D181 H183 F210 G305 Y308
Binding residue (residue number reindexed from 1)	M22 L131 H133 G141 F142 C143 D168 H170 F197 G292 Y295
Annotation score	1

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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External links

PDB	RCSB:7zzt, PDBe:7zzt, PDBj:7zzt
PDBsum	7zzt
PubMed	36262388
UniProt	Q92769\|HDAC2_HUMAN Histone deacetylase 2 (Gene Name=HDAC2)

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