3V5L

Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 542

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	d3v5la1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Tyrosine-protein kinase Itk/Tsk	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3v5la2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3v5lb1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Tyrosine-protein kinase Itk/Tsk	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3v5lb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3v5lc1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Tyrosine-protein kinase Itk/Tsk	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3v5lc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3v5ld1	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Tyrosine-protein kinase Itk/Tsk	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3v5ld2	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)	8039582	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039582	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039582	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039582	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	e3v5lA1	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	e3v5lB2	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	e3v5lC1	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	e3v5lD1	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	Tyrosine-protein kinase ITK/TSK	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 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 non-membrane spanning protein tyrosine kinase activity 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 cation binding metal ion binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response T cell receptor signaling pathway adaptive immune response developmental process multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation alpha-beta T cell differentiation T cell activation cell differentiation anatomical structure development alpha-beta T cell activation NK T cell differentiation T cell differentiation leukocyte differentiation gamma-delta T cell activation protein phosphorylation 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 defense response response to stress cellular defense response positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process intracellular signal transduction	cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle organelle nucleus cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR001849	Pleckstrin homology domain	Domain
A, B, C, D	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B, C, D	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR000980	SH2 domain	Domain
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR035583	Tyrosine-protein kinase ITK, SH3 domain	Domain
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D	IPR001562	Zinc finger, Btk motif	Conserved Site
A, B, C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR042785	Tyrosine-protein kinase ITK/TSK, catalytic domain	Domain
A, B, C, D	IPR001452	SH3 domain	Domain
A, B, C, D	IPR050198	Non-receptor tyrosine kinases involved in cell signaling	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q08881	lymphoproliferative syndrome 1 atopic eczema glioblastoma interstitial cystitis lung carcinoma Lymphoproliferative Syndrome, Ebv-Associated, Autosomal, 1 psoriasis Sjogren syndrome cutaneous lupus erythematosus hematopoietic and lymphoid system neoplasm invasive ductal breast carcinoma malignant glioma renal cell carcinoma ulcerative colitis gastric adenocarcinoma lymphoproliferative syndrome 1 atopic eczema glioblastoma interstitial cystitis lung carcinoma Lymphoproliferative Syndrome, Ebv-Associated, Autosomal, 1 psoriasis Sjogren syndrome cutaneous lupus erythematosus hematopoietic and lymphoid system neoplasm invasive ductal breast carcinoma malignant glioma renal cell carcinoma ulcerative colitis gastric adenocarcinoma IgA glomerulonephritis lung cancer metastatic melanoma

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.