2YDJ | pdb_00002ydj

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas

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)
B	d2ydjb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cell cycle checkpoint kinase chk1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ydja_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cell cycle checkpoint kinase chk1	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)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8033807	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8033807	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		e2ydjB2	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Pkinase	F:	ECOD (20:10:01)
A		e2ydjA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: C1-set	F:	ECOD (20:10:01)

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	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	SERINE/THREONINE-PROTEIN KINASE CHK1	protein binding binding protein domain specific 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 adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein binding binding protein domain specific 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 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 histone H3 kinase activity histone modifying activity histone H3T11 kinase activity histone kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of DNA recombination regulation of double-strand break repair regulation of cellular response to stress regulation of primary metabolic process regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair double-strand break repair DNA recombination regulation of macromolecule metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process signaling intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction apoptotic process involved in development developmental process anatomical structure development apoptotic process cell death programmed cell death regulation of cell cycle process negative regulation of biological process negative regulation of cell cycle G0 to G1 transition negative regulation of cell cycle process regulation of G0 to G1 transition negative regulation of G0 to G1 transition negative regulation of cellular process cell cycle process replicative senescence protein phosphorylation phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process peptidyl-threonine modification protein metabolic process protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process epigenetic regulation of gene expression negative regulation of metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process multicellular organismal process inner cell mass cell proliferation cell population proliferation developmental growth chordate embryonic development growth embryo development in utero embryonic development multicellular organism development embryo development ending in birth or egg hatching blastocyst growth blastocyst development regulation of cell cycle phase transition DNA damage checkpoint signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling cell cycle phase transition mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of cell population proliferation regulation of signaling regulation of signal transduction signal transduction by p53 class mediator regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator regulation of cell communication nucleus organization organelle organization centrosome separation microtubule cytoskeleton organization mitotic centrosome separation centrosome cycle mitotic nuclear division microtubule organizing center organization organelle fission regulation of mitotic centrosome separation nuclear division microtubule-based process cytoskeleton organization regulation of cellular component organization regulation of mitotic nuclear division negative regulation of cellular component organization regulation of organelle organization negative regulation of nuclear division negative regulation of organelle organization regulation of nuclear division negative regulation of mitotic nuclear division	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cytoplasm cytosol nucleoplasm chromatin protein-containing complex replication fork extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR034670	Checkpoint kinase 1, catalytic domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O14757	breast cancer breast carcinoma polyploidy malignant mesothelioma malignant pancreatic neoplasm medulloblastoma ovarian cancer adrenal cortex carcinoma peripheral nervous system disease primitive neuroectodermal tumor cancer tuberculosis endometriosis IgA glomerulonephritis lung adenocarcinoma breast cancer breast carcinoma polyploidy malignant mesothelioma malignant pancreatic neoplasm medulloblastoma ovarian cancer adrenal cortex carcinoma peripheral nervous system disease primitive neuroectodermal tumor cancer tuberculosis endometriosis IgA glomerulonephritis lung adenocarcinoma malignant ependymoma Malignant neoplasm of breast nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma atopic eczema peripheral neuropathy psoriasis cystic fibrosis ulcerative colitis glioblastoma invasive ductal breast carcinoma lung cancer malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor breast disease schizophrenia ductal breast carcinoma in situ hereditary breast carcinoma large cell medulloblastoma malignant colon neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.