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 | 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 | 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 | 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 | 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 | 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 | 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 |
