4WNP

Structure of ULK1 bound to a potent inhibitor

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4wnpa_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4wnpb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4wnpd_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4wnpc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	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	SCOP2 Family	Protein kinases catalytic domain-like	8062550	4003661	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein kinase-like (PK-like)	8062551	3000066	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062551	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062551	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062551	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	e4wnpA1	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)
B	Pkinase_Tyr	e4wnpB1	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)
D	Pkinase_Tyr	e4wnpD1	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)
C	Pkinase_Tyr	e4wnpC1	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)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	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, B, C, D	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, B, C, D	Serine/threonine-protein kinase ULK1	small GTPase binding protein binding binding enzyme binding GTPase binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding small GTPase binding protein binding binding enzyme binding GTPase binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding identical protein binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine/threonine kinase activity	multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation anatomical structure development regulation of biological quality system development developmental process regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of collateral sprouting regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process negative regulation of collateral sprouting regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size protein localization localization cellular localization cellular macromolecule localization macromolecule localization catabolic process macroautophagy cellular metabolic process autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of macroautophagy regulation of cellular catabolic process metabolic process regulation of metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus piecemeal microautophagy of the nucleus microautophagy nucleophagy protein-containing complex organization regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly protein phosphorylation phosphorylation primary metabolic process macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process peptidyl-threonine modification protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation protein autophosphorylation peptidyl-serine modification peptidyl-serine phosphorylation axon extension neuron projection extension regulation of protein modification process cellular biosynthetic process lipoprotein biosynthetic process lipoprotein metabolic process regulation of primary metabolic process protein lipidation regulation of lipoprotein metabolic process regulation of biosynthetic process regulation of protein lipidation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of macromolecule biosynthetic process positive regulation of organelle organization positive regulation of cellular component organization positive regulation of vacuole organization positive regulation of biological process autophagosome organization positive regulation of cellular metabolic process positive regulation of metabolic process positive regulation of autophagosome assembly positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy autophagosome assembly organelle assembly vacuole organization positive regulation of cellular component biogenesis regulation of autophagosome assembly regulation of vacuole organization regulation of organelle organization positive regulation of catabolic process organelle organization regulation of organelle assembly positive regulation of cellular catabolic process positive regulation of organelle assembly signaling response to cytokine regulation of signal transduction cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction regulation of signaling regulation of tumor necrosis factor-mediated signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication response to tumor necrosis factor regeneration neuron projection regeneration cellular response to stress response to stress response to starvation autophagy of mitochondrion negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation reticulophagy	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm cellular anatomical entity transferase complex cytosol membrane-bounded organelle intracellular organelle organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex intracellular anatomical structure catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm cellular anatomical entity transferase complex cytosol membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle vesicle mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane axon cell projection neuron projection plasma membrane bounded cell projection phagophore assembly site phagophore assembly site membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane omegasome membrane omegasome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045269	Serine/threonine-protein kinase Atg1-like	Family
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR048941	ATG1-like, MIT domain 2	Domain
A, B, C, D	IPR016237	Serine/threonine-protein kinase, Ulk1/Ulk2	Family
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR022708	Serine/threonine-protein kinase Atg1-like, tMIT domain	Domain
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O75385	gastrointestinal stromal tumor malignant glioma Pancreatic Neuroendocrine Tumor subependymal giant cell astrocytoma lung adenocarcinoma osteosarcoma pilocytic astrocytoma thrombocytopenia due to immune destruction malignant ependymoma ovarian mucinous adenocarcinoma renal cell carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.