8PYW

Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8038962	3001175	SCOP2B (2022-06-29)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Nucleoside diphosphate kinase B	DNA binding G-quadruplex DNA binding binding organic cyclic compound binding nucleic acid binding intermediate filament binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding DNA binding G-quadruplex DNA binding binding organic cyclic compound binding nucleic acid binding intermediate filament 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 nucleobase-containing compound kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding identical protein binding protein binding fatty acid binding organic acid binding lipid binding carboxylic acid binding monocarboxylic acid binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity guanyl nucleotide binding GDP binding guanyl ribonucleotide binding protein serine/threonine kinase activity catalytic activity, acting on a protein protein kinase activity phosphotransferase activity, alcohol group as acceptor phosphotransferase activity, nitrogenous group as acceptor protein histidine kinase activity enzyme binding	regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization ribose phosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process organic substance metabolic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process organonitrogen compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process organic cyclic compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process metabolic process UTP biosynthetic process nucleoside triphosphate metabolic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process regulation of developmental process epidermis development regulation of epidermis development tissue development cell adhesion response to growth hormone response to organic substance response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to oxygen-containing compound response to nitrogen compound positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process negative regulation of programmed cell death negative regulation of biological process negative regulation of apoptotic process negative regulation of cellular process homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular homeostasis chemical homeostasis response to glucose glucose homeostasis integrin-mediated signaling pathway cell surface receptor signaling pathway signaling cell communication signal transduction cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway GTP metabolic process GTP biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine nucleotide metabolic process purine nucleoside triphosphate biosynthetic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine-containing compound metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process positive regulation of keratinocyte differentiation regulation of epidermal cell differentiation regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process epithelium development regulation of multicellular organismal development epidermal cell differentiation animal organ development positive regulation of epidermis development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation positive regulation of multicellular organismal process regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation response to lipid response to fatty acid cellular response to fatty acid cellular response to lipid CTP biosynthetic process CTP metabolic process regulation of leukocyte differentiation myeloid leukocyte differentiation regulation of cell development negative regulation of cell differentiation regulation of immune system process negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process immune system process regulation of hemopoiesis negative regulation of multicellular organismal process leukocyte differentiation	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope cytoplasm organelle membrane cytosol ruffle perinuclear region of cytoplasm polymeric cytoskeletal fiber intermediate filament cytoskeleton cytoskeleton intracellular non-membrane-bounded organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle cell periphery membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001564	Nucleoside diphosphate kinase	Family
A, B, C, D, E A, B, C, D, E, F	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P22392	colorectal cancer benign mesothelioma Colorectal Neoplasms osteoarthritis susceptibility 1 ovarian neoplasm drug-induced liver injury mesothelioma colorectal carcinoma heart disease osteoarthritis ovarian cancer

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 R01GM133198.