Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6ODB

Crystal structure of HDAC8 in complex with compound 3

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000118	cellular_component	histone deacetylase complex
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000228	cellular_component	nuclear chromosome
A	0004407	molecular_function	histone deacetylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0005737	cellular_component	cytoplasm
A	0006325	biological_process	chromatin organization
A	0007064	biological_process	mitotic sister chromatid cohesion
A	0016787	molecular_function	hydrolase activity
A	0030544	molecular_function	Hsp70 protein binding
A	0031397	biological_process	negative regulation of protein ubiquitination
A	0031507	biological_process	heterochromatin formation
A	0031647	biological_process	regulation of protein stability
A	0032204	biological_process	regulation of telomere maintenance
A	0033558	molecular_function	protein lysine deacetylase activity
A	0046872	molecular_function	metal ion binding
A	0051879	molecular_function	Hsp90 protein binding
A	0140297	molecular_function	DNA-binding transcription factor binding
A	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
A	0160008	molecular_function	protein decrotonylase activity
A	0160009	molecular_function	histone decrotonylase activity
B	0000118	cellular_component	histone deacetylase complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000228	cellular_component	nuclear chromosome
B	0004407	molecular_function	histone deacetylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0005737	cellular_component	cytoplasm
B	0006325	biological_process	chromatin organization
B	0007064	biological_process	mitotic sister chromatid cohesion
B	0016787	molecular_function	hydrolase activity
B	0030544	molecular_function	Hsp70 protein binding
B	0031397	biological_process	negative regulation of protein ubiquitination
B	0031507	biological_process	heterochromatin formation
B	0031647	biological_process	regulation of protein stability
B	0032204	biological_process	regulation of telomere maintenance
B	0033558	molecular_function	protein lysine deacetylase activity
B	0046872	molecular_function	metal ion binding
B	0051879	molecular_function	Hsp90 protein binding
B	0140297	molecular_function	DNA-binding transcription factor binding
B	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
B	0160008	molecular_function	protein decrotonylase activity
B	0160009	molecular_function	histone decrotonylase activity
C	0000118	cellular_component	histone deacetylase complex
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000228	cellular_component	nuclear chromosome
C	0004407	molecular_function	histone deacetylase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
C	0005737	cellular_component	cytoplasm
C	0006325	biological_process	chromatin organization
C	0007064	biological_process	mitotic sister chromatid cohesion
C	0016787	molecular_function	hydrolase activity
C	0030544	molecular_function	Hsp70 protein binding
C	0031397	biological_process	negative regulation of protein ubiquitination
C	0031507	biological_process	heterochromatin formation
C	0031647	biological_process	regulation of protein stability
C	0032204	biological_process	regulation of telomere maintenance
C	0033558	molecular_function	protein lysine deacetylase activity
C	0046872	molecular_function	metal ion binding
C	0051879	molecular_function	Hsp90 protein binding
C	0140297	molecular_function	DNA-binding transcription factor binding
C	0141221	molecular_function	histone deacetylase activity, hydrolytic mechanism
C	0160008	molecular_function	protein decrotonylase activity
C	0160009	molecular_function	histone decrotonylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	binding site for residue M8G A 401

Chain	Residue
A	LYS33
A	ASP267
A	MET274
A	TYR306
A	ZN402
A	HOH522
A	TYR100
A	ASP101
A	HIS142
A	HIS143
A	GLY151
A	PHE152
A	ASP178
A	HIS180

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 402

Chain	Residue
A	ASP178
A	HIS180
A	ASP267
A	M8G401

site_id	AC3
Number of Residues	6
Details	binding site for residue K A 403

Chain	Residue
A	PHE189
A	THR192
A	VAL195
A	TYR225
A	HOH517
A	HOH538

site_id	AC4
Number of Residues	5
Details	binding site for residue K A 404

Chain	Residue
A	ASP176
A	ASP178
A	HIS180
A	SER199
A	LEU200

site_id	AC5
Number of Residues	3
Details	binding site for residue GOL A 405

Chain	Residue
A	ALA68
A	HIS71
B	GOL405

site_id	AC6
Number of Residues	7
Details	binding site for residue GOL A 406

Chain	Residue
A	SER215
A	VAL217
A	GLY218
A	LEU219
A	GOL407
C	ASP343
C	THR349

site_id	AC7
Number of Residues	6
Details	binding site for residue GOL A 407

Chain	Residue
A	THR211
A	GLY212
A	ASP213
A	SER215
A	ASP216
A	GOL406

site_id	AC8
Number of Residues	11
Details	binding site for residue M8G B 401

Chain	Residue
B	LYS33
B	ASP101
B	HIS142
B	HIS143
B	PHE152
B	ASP178
B	HIS180
B	ASP267
B	MET274
B	TYR306
B	ZN402

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	ASP178
B	HIS180
B	ASP267
B	M8G401

site_id	AD1
Number of Residues	5
Details	binding site for residue K B 403

Chain	Residue
B	PHE189
B	THR192
B	VAL195
B	TYR225
B	HOH518

site_id	AD2
Number of Residues	5
Details	binding site for residue K B 404

Chain	Residue
B	ASP176
B	ASP178
B	HIS180
B	SER199
B	LEU200

site_id	AD3
Number of Residues	4
Details	binding site for residue GOL B 405

Chain	Residue
A	GOL405
B	GLY99
B	TYR100
B	ALA104

site_id	AD4
Number of Residues	12
Details	binding site for residue M8G C 401

Chain	Residue
C	LYS33
C	ASP101
C	HIS142
C	HIS143
C	PHE152
C	ASP178
C	HIS180
C	PHE208
C	ASP267
C	MET274
C	TYR306
C	ZN402

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN C 402

Chain	Residue
C	ASP178
C	HIS180
C	ASP267
C	M8G401

site_id	AD6
Number of Residues	5
Details	binding site for residue K C 403

Chain	Residue
C	PHE189
C	THR192
C	VAL195
C	TYR225
C	HOH506

site_id	AD7
Number of Residues	5
Details	binding site for residue K C 404

Chain	Residue
C	LEU200
C	ASP176
C	ASP178
C	HIS180
C	SER199

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	620
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17721440","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15242608","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)