Structure of PDB 6z2k Chain I Binding Site BS02

Receptor Information
>6z2k Chain I (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPH
KANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLF
EFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIV
LAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPG
TGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAV
VLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRN
VARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNE
YLEKIKQRLFENLRMLPHA
Ligand information
Ligand IDIHP
InChIInChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
InChIKeyIMQLKJBTEOYOSI-GPIVLXJGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
ACDLabs 12.01
OpenEye OEToolkits 2.0.7		C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
CACTVS 3.385O[P](O)(=O)O[C@@H]1[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
FormulaC6 H18 O24 P6
NameINOSITOL HEXAKISPHOSPHATE;
MYO-INOSITOL HEXAKISPHOSPHATE;
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
ChEMBLCHEMBL1233511
DrugBankDB14981
ZINCZINC000169289809
PDB chain6z2k Chain D Residue 901 [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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PDB6z2k The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure.
Resolution4.5 Å
Binding residue
(original residue number in PDB)		G27 K31
Binding residue
(residue number reindexed from 1)		G20 K24
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0001222 transcription corepressor binding
GO:0002039 p53 binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003714 transcription corepressor activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0019899 enzyme binding
GO:0031492 nucleosomal DNA binding
GO:0033558 protein lysine deacetylase activity
GO:0035851 Krueppel-associated box domain binding
GO:0042826 histone deacetylase binding
GO:0051059 NF-kappaB binding
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0070888 E-box binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006346 DNA methylation-dependent heterochromatin formation
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006476 protein deacetylation
GO:0007492 endoderm development
GO:0007623 circadian rhythm
GO:0008284 positive regulation of cell population proliferation
GO:0009913 epidermal cell differentiation
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010832 negative regulation of myotube differentiation
GO:0021766 hippocampus development
GO:0030182 neuron differentiation
GO:0030336 negative regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0031507 heterochromatin formation
GO:0032922 circadian regulation of gene expression
GO:0036120 cellular response to platelet-derived growth factor stimulus
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:0043124 negative regulation of canonical NF-kappaB signal transduction
GO:0043922 negative regulation by host of viral transcription
GO:0045814 negative regulation of gene expression, epigenetic
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:0048511 rhythmic process
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0048709 oligodendrocyte differentiation
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0060766 negative regulation of androgen receptor signaling pathway
GO:0060789 hair follicle placode formation
GO:0061029 eyelid development in camera-type eye
GO:0061198 fungiform papilla formation
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:1902455 negative regulation of stem cell population maintenance
GO:1902459 positive regulation of stem cell population maintenance
GO:2000273 positive regulation of signaling receptor activity
GO:2000736 regulation of stem cell differentiation
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000785 chromatin
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016581 NuRD complex
GO:0017053 transcription repressor complex
GO:0032991 protein-containing complex
GO:0043025 neuronal cell body
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:6z2k, PDBe:6z2k, PDBj:6z2k
PDBsum6z2k
PubMed32591534
UniProtQ13547|HDAC1_HUMAN Histone deacetylase 1 (Gene Name=HDAC1)

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