4WHK | pdb_00004whk

A New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Polo-box domain	8041915	3000394	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Polo-box domain	8041914	3000394	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	POLO_box	e4whkA2	A: a+b two layers	X: RIP/Polo-box domain	H: Polo-box domain (From Topology)	T: Polo-box domain	F: POLO_box	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1120.30	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain	POLO box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00659	POLO box duplicated region (POLO_box)	POLO box duplicated region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	C6H5(CH2)8-DERIVATIZED PEPTIDE INHIBITOR	-	-	-
A	Serine/threonine-protein kinase PLK1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding microtubule binding protein binding tubulin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein serine kinase activity cation binding magnesium ion binding metal ion binding protein-containing complex binding anaphase-promoting complex binding kinase binding enzyme binding protein kinase binding protein serine/threonine kinase activity	cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination DNA damage response regulation of response to stimulus metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of chromosome segregation regulation of cell cycle phase transition regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of cell cycle process chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition protein destabilization regulation of protein stability regulation of biological quality regulation of cytoskeleton organization microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly cellular component biogenesis cellular component assembly regulation of mitotic spindle assembly mitotic sister chromatid segregation microtubule cytoskeleton organization involved in mitosis spindle organization mitotic nuclear division organelle assembly organelle fission regulation of microtubule-based process regulation of spindle organization regulation of cellular component biogenesis spindle assembly mitotic spindle organization regulation of spindle assembly mitotic spindle assembly nuclear division regulation of organelle assembly microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization mitotic chromosome condensation chromosome condensation membrane organization cellular component disassembly nuclear membrane disassembly membrane disassembly nuclear membrane organization mitotic nuclear membrane disassembly nucleus organization nuclear envelope organization endomembrane system organization sister chromatid cohesion localization protein localization to organelle macromolecule localization protein localization to nucleus intracellular protein localization protein localization to nuclear envelope positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein modification process regulation of catalytic activity regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of ubiquitin protein ligase activity positive regulation of molecular function positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification positive regulation of catalytic activity positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of cytokinesis cytokinesis regulation of cell division cell division establishment of organelle localization cellular localization spindle localization establishment or maintenance of cell polarity establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation organelle localization establishment of localization in cell establishment of localization establishment of cell polarity establishment of mitotic spindle orientation protein phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification double-strand break repair via nonhomologous end joining double-strand break repair via alternative nonhomologous end joining RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cell cycle G2/M phase transition G2/M transition of mitotic cell cycle regulation of localization protein localization to cell periphery regulation of protein localization regulation of protein localization to cell periphery regulation of protein localization to cell cortex protein localization to cell cortex meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation female meiotic nuclear division meiotic nuclear division female meiosis chromosome segregation positive regulation of protein localization to nucleus regulation of protein localization to nucleus positive regulation of protein localization microtubule bundle formation cytoskeleton-dependent cytokinesis mitotic cytokinesis establishment of protein localization negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death protein localization to chromatin protein localization to chromosome spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction mitotic sister chromatid separation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling negative regulation of cellular component organization regulation of mitotic sister chromatid segregation regulation of chromosome separation negative regulation of mitotic nuclear division regulation of mitotic sister chromatid separation signaling spindle assembly checkpoint signaling negative regulation of mitotic metaphase/anaphase transition negative regulation of chromosome separation negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle DNA damage checkpoint signaling mitotic G2 DNA damage checkpoint signaling mitotic G2/M transition checkpoint mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling regulation of G2/M transition of mitotic cell cycle DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle synaptonemal complex disassembly synaptonemal complex organization Golgi inheritance organelle inheritance Golgi organization microtubule organizing center organization centrosome cycle meiosis I meiosis I cell cycle process homologous chromosome segregation regulation of anaphase-promoting complex-dependent catabolic process anaphase-promoting complex-dependent catabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone cytoplasm cytosol protein-containing complex intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton spindle midzone cytoplasm cytosol protein-containing complex chromosome chromosomal region kinetochore chromosome, centromeric region outer kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromatin mitotic spindle mitotic spindle pole midbody centrosome microtubule organizing center centriolar satellite centriole membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen condensed nuclear chromosome nuclear chromosome synaptonemal structure synaptonemal complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000719	Protein kinase domain	Domain
A	IPR000959	POLO box domain	Domain
A	IPR033695	Second polo-box domain	Domain
A	IPR033702	Polo-like kinase 1, catalytic domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR036947	POLO box domain superfamily	Homologous Superfamily
A	IPR033701	First polo-box domain	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P53350	malignant glioma leukemia mixed glioma atypical teratoid rhabdoid tumor cancer hepatocellular carcinoma malignant mesothelioma non-small cell lung carcinoma squamous cell lung carcinoma breast cancer glioblastoma invasive ductal breast carcinoma lung adenocarcinoma medulloblastoma osteosarcoma malignant glioma leukemia mixed glioma atypical teratoid rhabdoid tumor cancer hepatocellular carcinoma malignant mesothelioma non-small cell lung carcinoma squamous cell lung carcinoma breast cancer glioblastoma invasive ductal breast carcinoma lung adenocarcinoma medulloblastoma osteosarcoma breast carcinoma glioma large cell medulloblastoma psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	56A	Parent Component: HIS
B	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
B	TPO	Parent Component: THR RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 , AA0038 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109 , O-phospho-L-threonine MOD:00047
B	YAC	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 , AA0038

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.