2LGC | pdb_00002lgc

Joint NMR and X-ray refinement reveals the structure of a novel dibenzo[a,d]cycloheptenone inhibitor/p38 MAP kinase complex in solution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2lgca1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	MAP kinase p38	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2lgca2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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)	8033039	3000066	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	Pkinase_Tyr	e2lgcA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

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 (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

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	Mitogen-activated protein kinase 14	protein phosphatase binding phosphatase binding protein binding binding enzyme 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 protein phosphatase binding phosphatase binding protein binding binding enzyme 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 protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity MAP kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups MAP kinase kinase activity protein serine/threonine/tyrosine kinase activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NFAT protein binding protein serine kinase activity kinase binding mitogen-activated protein kinase p38 binding protein kinase binding mitogen-activated protein kinase binding	D-glucose import hexose transmembrane transport transport carbohydrate transport establishment of localization transmembrane transport localization D-glucose transmembrane transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport cellular response to stimulus stress-induced premature senescence cellular response to stress D-glucose import hexose transmembrane transport transport carbohydrate transport establishment of localization transmembrane transport localization D-glucose transmembrane transport cellular process monosaccharide transmembrane transport carbohydrate transmembrane transport cellular response to stimulus stress-induced premature senescence cellular response to stress response to stimulus response to stress cellular senescence regulation of biological process regulation of cellular process signaling biological regulation p38MAPK cascade intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade signal transduction developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation myoblast differentiation positive regulation of cellular process placenta development animal organ development regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process multicellular organismal process regulation of growth positive regulation of cell population proliferation regulation of cardiac muscle tissue growth developmental growth cardiac muscle cell proliferation organ growth striated muscle tissue development multicellular organism development positive regulation of cardiac muscle cell proliferation regulation of organ growth regulation of heart growth 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 heart growth system development striated muscle cell proliferation heart development heart growth regulation of multicellular organismal development cell population proliferation regulation of developmental growth cardiac muscle tissue development positive regulation of organ growth growth 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 skeletal system development bone development positive regulation of molecular function regulation of molecular function positive regulation of cyclase activity regulation of catalytic activity positive regulation of catalytic activity apoptotic process cell death programmed cell death negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication response to ionizing radiation cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus cell aggregation connective tissue development cartilage condensation anatomical structure morphogenesis skeletal system morphogenesis animal organ morphogenesis cartilage development regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport import into nucleus regulation of protein import into nucleus establishment of localization in cell protein import into nucleus positive regulation of intracellular transport intracellular protein localization regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of protein localization to organelle positive regulation of transport protein transport regulation of cellular localization macromolecule localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process small molecule metabolic process primary metabolic process glucose metabolic process response to light stimulus response to UV response to UV-B cellular response to UV-B cellular response to light stimulus cellular response to UV chemotaxis taxis response to chemical response to external stimulus locomotion regulation of body fluid levels wound healing cell activation hemostasis blood coagulation coagulation regulation of biological quality response to wounding platelet activation hippo signaling negative regulation of intracellular signal transduction regulation of intracellular signal transduction negative regulation of hippo signaling regulation of hippo signaling regulation of striated muscle cell differentiation muscle cell differentiation myotube differentiation positive regulation of myotube differentiation positive regulation of striated muscle cell differentiation regulation of myotube differentiation positive regulation of muscle cell differentiation regulation of muscle cell differentiation striated muscle cell differentiation cell morphogenesis homeostatic process cell development regulation of cell development regulation of immune system process myeloid cell homeostasis erythrocyte homeostasis hemopoiesis regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells biological process involved in interspecies interaction between organisms cellular response to lipoteichoic acid response to other organism response to oxygen-containing compound response to lipoteichoic acid cellular response to molecule of bacterial origin cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin cell surface receptor protein serine/threonine kinase signaling pathway enzyme-linked receptor protein signaling pathway regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response inflammatory response to antigenic stimulus regulation of response to stress negative regulation of inflammatory response to antigenic stimulus defense response immune response negative regulation of immune response regulation of inflammatory response to antigenic stimulus regulation of inflammatory response negative regulation of immune system process negative regulation of response to external stimulus negative regulation of defense response regulation of immune response inflammatory response positive regulation of cellular component organization regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion cell-cell fusion cellular component organization cellular component organization or biogenesis syncytium formation positive regulation of myoblast fusion myoblast fusion regulation of myoblast fusion positive regulation of syncytium formation by plasma membrane fusion syncytium formation by plasma membrane fusion anatomical structure formation involved in morphogenesis regulation of cell adhesion regulation of synaptic membrane adhesion regulation of synapse organization cell adhesion cell junction organization cell-cell adhesion regulation of synapse structure or activity regulation of cell-cell adhesion synapse organization synaptic membrane adhesion response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor chondrocyte differentiation regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA catabolic process mRNA stabilization mRNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process negative regulation of RNA metabolic process catabolic process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process 3'-UTR-mediated mRNA stabilization regulation of mRNA catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process positive regulation of DNA-templated transcription RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage ossification osteoblast differentiation blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis blood vessel development stress-activated MAPK cascade stress-activated protein kinase signaling cascade response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway response to lipopolysaccharide cellular response to lipid regulation of ossification skeletal muscle organ development skeletal muscle tissue development muscle organ development regulation of interleukin-12 production cytokine production regulation of cytokine production interleukin-12 production positive regulation of interleukin-12 production positive regulation of cytokine production reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process fat cell differentiation positive regulation of brown fat cell differentiation positive regulation of fat cell differentiation regulation of brown fat cell differentiation brown fat cell differentiation regulation of fat cell differentiation response to hormone response to peptide hormone response to insulin response to nitrogen compound regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process lipid modification organic acid metabolic process fatty acid oxidation lipid oxidation monocarboxylic acid metabolic process lipid metabolic process response to muramyl dipeptide myeloid leukocyte differentiation osteoclast differentiation leukocyte differentiation positive regulation of D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose import positive regulation of D-glucose import regulation of transmembrane transport regulation of D-glucose transmembrane transport stem cell differentiation cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor receptor signaling pathway cellular response to virus response to virus response to mechanical stimulus response to muscle stretch response to nutrient levels response to dietary excess energy homeostasis	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol synapse cell junction glutamatergic synapse mitochondrion intracellular vesicle ficolin-1-rich granule endomembrane system cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle extracellular region vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003527	Mitogen-activated protein (MAP) kinase, conserved site	Conserved Site
A	IPR000719	Protein kinase domain	Domain
A	IPR050117	Mitogen-activated protein (MAP) kinase	Family
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR008352	Mitogen-activated protein (MAP) kinase HOG-like	Family
A	IPR038784	Mitogen-activated protein kinase 14	Family
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q16539	cardiomyopathy chronic myelogenous leukemia, BCR-ABL1 positive liver cancer cholestasis lung benign neoplasm lymphoplasmacytic lymphoma Malignant neoplasm of lung attention deficit hyperactivity disorder, inattentive type ovarian cancer coronary artery disease primary biliary cholangitis rheumatoid arthritis Gaucher disease subependymal giant cell astrocytoma liver neoplasm cardiomyopathy chronic myelogenous leukemia, BCR-ABL1 positive liver cancer cholestasis lung benign neoplasm lymphoplasmacytic lymphoma Malignant neoplasm of lung attention deficit hyperactivity disorder, inattentive type ovarian cancer coronary artery disease primary biliary cholangitis rheumatoid arthritis Gaucher disease subependymal giant cell astrocytoma liver neoplasm lung cancer malignant ependymoma myocardial ischemia atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma pilocytic astrocytoma progressive supranuclear palsy extrahepatic cholestasis schizophrenia glioblastoma large cell medulloblastoma lung adenocarcinoma malignant glioma medulloblastoma osteosarcoma plantar wart psoriasis gastric adenocarcinoma spondyloarthropathy

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.