4ZJJ

PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide

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	d4zjja_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	pak1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4zjjc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	pak1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4zjjb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	pak1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4zjjd_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	pak1	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)	8034489	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8034489	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8034489	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8034489	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	e4zjjA1	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	e4zjjC1	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	e4zjjB1	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	e4zjjD1	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)
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)
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)

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 PAK 1	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 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 identical protein binding protein binding collagen binding protein-containing complex binding protein serine kinase activity cytoskeletal protein binding gamma-tubulin binding tubulin binding protein serine/threonine kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process epithelium development tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process epithelium development tube development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis morphogenesis of a branching structure anatomical structure development epithelial tube morphogenesis morphogenesis of a branching epithelium regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway apoptotic process cell death programmed cell death regulation of signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process positive regulation of cellular process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization hepatocyte growth factor receptor signaling pathway cell migration cell motility protein autophosphorylation positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization positive regulation of cellular component organization microtubule cytoskeleton organization cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization positive regulation of protein polymerization protein-containing complex assembly protein polymerization positive regulation of microtubule polymerization or depolymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process microtubule polymerization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of microtubule polymerization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization microtubule-based process supramolecular fiber organization regulation of microtubule cytoskeleton organization positive regulation of cell communication positive regulation of signal transduction regulation of catalytic activity regulation of transferase activity regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of MAP kinase activity positive regulation of MAPK cascade positive regulation of intracellular signal transduction positive regulation of JUN kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity positive regulation of response to stimulus positive regulation of molecular function positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of JUN kinase activity positive regulation of signaling protein localization localization cellular localization protein localization to cytoplasmic stress granule protein localization to organelle cellular macromolecule localization macromolecule localization negative regulation of cell population proliferation cell population proliferation negative regulation of biological process detection of cell density detection of biotic stimulus response to biotic stimulus detection of stimulus negative regulation of cell proliferation involved in contact inhibition regulation of cell population proliferation negative regulation of cellular process contact inhibition regulation of neuron projection development axonogenesis cellular developmental process regulation of developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of axonogenesis cell differentiation regulation of anatomical structure morphogenesis system development plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of actin filament-based process regulation of actin cytoskeleton organization positive regulation of microtubule nucleation regulation of microtubule nucleation microtubule nucleation positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus response to lectin defense response to other organism cellular response to lectin positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus innate immune response activating cell surface receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont stimulatory C-type lectin receptor signaling pathway immune system process positive regulation of cell population proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion wound healing response to wounding secretion by cell exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport intracellular receptor signaling pathway response to lipid positive regulation of intracellular estrogen receptor signaling pathway hormone-mediated signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway 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 estrogen receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway immune response-regulating cell surface receptor signaling pathway involved in phagocytosis import into cell Fc-gamma receptor signaling pathway involved in phagocytosis Fc receptor signaling pathway phagocytosis Fc-gamma receptor signaling pathway Fc receptor mediated stimulatory signaling pathway immune effector process endocytosis regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly stress fiber assembly regulation of actin filament organization actomyosin structure organization actin filament organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly chromatin organization chromatin remodeling	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cell-cell junction anchoring junction cell junction membrane-bounded organelle nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system organelle envelope nuclear envelope organelle membrane cytosol somatodendritic compartment dendrite dendritic tree neuron projection chromosome ruffle polymeric cytoskeletal fiber actin filament actin cytoskeleton cytoskeleton axon intercalated disc cell-cell contact zone focal adhesion cell-substrate junction plasma membrane leading edge membrane cell periphery ruffle membrane plasma membrane region cell projection membrane centrosome microtubule organizing center microtubule cytoskeleton membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050285	STE20 Serine/Threonine-Protein Kinase	Family
A, B, C, D	IPR000719	Protein kinase domain	Domain
A, B, C, D	IPR036936	CRIB domain superfamily	Homologous Superfamily
A, B, C, D	IPR000095	CRIB domain	Domain
A, B, C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B, C, D	IPR033923	p21 activated kinase binding 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: Q13153	renal cell carcinoma breast carcinoma proteinuria collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma Mammary Neoplasms melanoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor Pick disease cystic fibrosis large cell medulloblastoma renal cell carcinoma breast carcinoma proteinuria collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma Mammary Neoplasms melanoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor Pick disease cystic fibrosis large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor pilocytic astrocytoma renal carcinoma subependymal giant cell astrocytoma epilepsy lung cancer malignant glioma malignant pancreatic neoplasm medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma breast cancer primitive neuroectodermal tumor clear cell renal carcinoma cutaneous melanoma tuberculosis glioblastoma lung carcinoma malignant mesothelioma

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.