6YKD | pdb_00006ykd

Human Pim-1 kinase in complex with an inhibitor identified by virtual screening

External Resource: Annotation

Domain Annotation: SCOP2 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	Protein kinase-like (PK-like)	8044193	3000066	SCOP2B (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (utative)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Serine/threonine-protein kinase pim-1	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H2AS121 kinase activity histone modifying activity histone H2A kinase activity catalytic activity histone kinase activity AMP-activated protein kinase activity cation binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H2AS121 kinase activity histone modifying activity histone H2A kinase activity catalytic activity histone kinase activity AMP-activated protein kinase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding DNA-dependent protein kinase activity histone H3T45 kinase activity histone H3 kinase activity eukaryotic translation initiation factor 2alpha kinase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transcription factor binding protein binding histone H3T6 kinase activity histone H3T3 kinase activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity molecular function regulator activity protein kinase activator activity kinase regulator activity histone H2BS14 kinase activity histone H2B kinase activity histone H3S57 kinase activity Rho-dependent protein serine/threonine kinase activity histone H2AT120 kinase activity histone H2AXS139 kinase activity histone H2AX kinase activity histone H4S1 kinase activity histone H4 kinase activity protein serine kinase activity histone H3T11 kinase activity histone H3S28 kinase activity 3-phosphoinositide-dependent protein kinase activity histone H2BS36 kinase activity histone H2AS1 kinase activity ribosomal protein S6 kinase activity histone H3S10 kinase activity ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization multicellular organismal process regulation of growth regulation of cellular process positive regulation of cell population proliferation regulation of developmental process regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation positive regulation of biological process organ growth regulation of protein stability biological regulation regulation of biological quality protein stabilization multicellular organismal process regulation of growth regulation of cellular process positive regulation of cell population proliferation regulation of developmental process regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation positive regulation of biological process organ growth striated muscle tissue development positive regulation of developmental process multicellular organism development positive regulation of cardiac muscle cell proliferation regulation of organ growth regulation of heart growth anatomical structure development regulation of cardiac muscle cell proliferation muscle cell proliferation regulation of multicellular organismal process cardiac muscle tissue growth muscle tissue development positive regulation of developmental growth positive regulation of cellular process positive regulation of heart growth system development striated muscle cell proliferation developmental process heart development regulation of biological process heart growth regulation of multicellular organismal development cell population proliferation regulation of developmental growth cardiac muscle tissue development positive regulation of organ growth growth animal organ development tissue development circulatory system development positive regulation of growth regulation of cell population proliferation positive regulation of cardiac muscle tissue growth positive regulation of multicellular organismal process cellular process apoptotic process cell death programmed cell death positive regulation of cardioblast proliferation positive regulation of cell proliferation involved in heart morphogenesis heart morphogenesis cardioblast proliferation regulation of cardioblast proliferation animal organ morphogenesis animal organ formation heart formation anatomical structure morphogenesis cell proliferation involved in heart morphogenesis anatomical structure formation involved in morphogenesis regulation of cell proliferation involved in heart morphogenesis protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein kinase activity positive regulation of protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process regulation of stem cell proliferation cellular developmental process hemopoiesis cell development stem cell proliferation cell differentiation hematopoietic stem cell proliferation regulation of hematopoietic stem cell proliferation negative regulation of DNA-binding transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process negative regulation of molecular function nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle regulation of localization regulation of transport transport regulation of transmembrane transporter activity establishment of localization regulation of transporter activity transmembrane transport localization regulation of transmembrane transport negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus response to stimulus regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus negative regulation of response to stimulus immune response response to other organism defense response regulation of innate immune response negative regulation of immune response defense response to symbiont response to external stimulus regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response cellular response to stimulus response to nutrient levels intracellular receptor signaling pathway response to lipid signaling response to vitamin hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to vitamin D cellular response to endogenous stimulus response to vitamin D response to hormone signal transduction cellular response to hormone stimulus response to endogenous stimulus response to nutrient response to oxygen-containing compound cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to chemical stimulus cellular response to vitamin response to chemical cellular response to lipid cellular response to nutrient nuclear receptor-mediated signaling pathway positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of cyclin-dependent protein serine/threonine kinase activity positive regulation of cyclin-dependent protein kinase activity positive regulation of cell cycle positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of TORC1 signaling positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of cell communication TORC1 signaling positive regulation of signaling response to type II interferon response to cytokine cellular response to type II interferon response to peptide cellular response to cytokine stimulus fat cell differentiation positive regulation of brown fat cell differentiation positive regulation of fat cell differentiation regulation of cell differentiation regulation of brown fat cell differentiation positive regulation of cell differentiation brown fat cell differentiation regulation of fat cell differentiation cellular detoxification detoxification cellular response to toxic substance response to toxic substance positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen cell periphery plasma membrane membrane nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017348	Serine/threonine-protein kinase pim-1/2/3	Family
A	IPR000719	Protein kinase domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR051138	PIM Serine/Threonine Kinase	Family
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P11309	glioblastoma allergic contact dermatitis prostate intraepithelial neoplasia breast carcinoma giant cell glioblastoma pyelonephritis breast cancer lung cancer Malignant neoplasm of breast ovarian cancer rheumatoid arthritis colorectal adenocarcinoma lung carcinoma malignant pancreatic neoplasm precancerous condition glioblastoma allergic contact dermatitis prostate intraepithelial neoplasia breast carcinoma giant cell glioblastoma pyelonephritis breast cancer lung cancer Malignant neoplasm of breast ovarian cancer rheumatoid arthritis colorectal adenocarcinoma lung carcinoma malignant pancreatic neoplasm precancerous condition atypical teratoid rhabdoid tumor cancer esophageal adenocarcinoma malignant mesothelioma osteosarcoma congenital diaphragmatic hernia cystic fibrosis exocrine pancreatic carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.