3EN4

Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with PP121, a multitargeted kinase 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3en4b_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	c-src tyrosine kinase	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
A	d3en4a_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	c-src tyrosine kinase	bantam,chickens (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8036665	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8036665	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)
B	Pkinase_Tyr	e3en4B1	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)
A	Pkinase_Tyr	e3en4A1	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)
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)
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, B	PF07714	Protein tyrosine and serine/threonine kinase (PK_Tyr_Ser-Thr)	Protein tyrosine and serine/threonine kinase	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosph ...	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [1]; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Proto-oncogene tyrosine-protein kinase Src	protein binding binding signaling receptor binding protein phosphatase binding phosphatase binding enzyme binding protein tyrosine kinase activity 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 protein binding binding signaling receptor binding protein phosphatase binding phosphatase binding enzyme binding protein tyrosine kinase activity 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 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 non-membrane spanning protein tyrosine kinase activity tetrapyrrole binding heme binding connexin binding	developmental process cellular developmental process cell differentiation cellular process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism developmental process cellular developmental process cell differentiation cellular process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus cellular response to stimulus regulation of cellular process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway negative regulation of cellular process signal transduction intrinsic apoptotic signaling pathway regulation of biological process regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation cell death negative regulation of signal transduction negative regulation of intrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway cell surface receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway ERBB signaling pathway epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway cell adhesion extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway intracellular receptor signaling pathway response to lipid progesterone receptor signaling pathway hormone-mediated signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to organic cyclic compound cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway cell cycle regulation of cell cycle	cellular anatomical structure cell junction membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope mitochondrial envelope organelle cellular anatomical structure cell junction membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope mitochondrial envelope organelle cytoplasm organelle membrane anchoring junction focal adhesion cell-substrate junction cytosol cell periphery plasma membrane protein-containing complex cytoskeleton membraneless organelle intracellular membraneless organelle perinuclear region of cytoplasm endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR000980	SH2 domain	Domain
A, B	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR001452	SH3 domain	Domain
A, B	IPR050198	Non-receptor tyrosine kinases involved in cell signaling	Family

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.