5K4L | pdb_00005k4l

Crystal structure of KDM5A in complex with a naphthyridone inhibitor

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	ARID-like	8074032	3001026	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARID-like	8074032	3001026	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		e5k4lB1	A: UBC-like	X: UBC-like	H: UBC-like	T: BRE	F:	ECOD (20:10:01)
A		e5k4lA1	A: UBC-like	X: UBC-like	H: UBC-like	T: BRE	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B	1.10.150.60	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	1.10.150.60	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21323	Lysine-specific demethylase 5, C-terminal helical domain (KDM5_C-hel)	Lysine-specific demethylase 5, C-terminal helical domain	This is the C-terminal helical domain from Lysine-specific demethylase 5 subfamily (KDM5), which is localised between the Jumonji C (JmjC) domain and the C5HC2 zinc finger motif (Pfam:PF02928) [1-5].	Domain
A, B	PF02928	C5HC2 zinc finger (zf-C5HC2)	C5HC2 zinc finger	Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [1]. This domain may have a DNA binding function.	Domain
A, B	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain
A, B	PF02375	jmjN domain (JmjN)	jmjN domain	-	Family
A, B	PF01388	ARID/BRIGHT DNA binding domain (ARID)	ARID/BRIGHT DNA binding domain	This domain is know as ARID for AT-Rich Interaction Domain [1], and also known as the BRIGHT domain [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth F], D [auth G]	Unknown Peptide	-	-	-
A, B	Lysine-specific demethylase 5A	protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein binding binding histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding chromatin DNA binding catalytic activity, acting on a protein protein demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen dioxygenase activity oxidoreductase activity histone H3 demethylase activity 2-oxoglutarate-dependent dioxygenase activity histone H3K4 demethylase activity	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription negative regulation of biological process cellular component biogenesis cellular component assembly negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process facultative heterochromatin formation negative regulation of gene expression, epigenetic positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm chromatin chromosome protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR048615	Lysine-specific demethylase 5, C-terminal helical domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR003349	JmjN domain	Domain
A, B	IPR001606	ARID DNA-binding domain	Domain
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR047970	Lysine-specific demethylase 5A, second PHD finger	Domain
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, B	IPR047973	Lysine-specific demethylase 5A, first PHD-finger	Domain
A, B	IPR013637	Lysine-specific demethylase-like domain	Domain
A, B	IPR047972	Lysine-specific demethylase 5A, third PHD-finger	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR004198	Zinc finger, C5HC2-type	Domain
A, B	IPR036431	ARID DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR047974	Lysine-specific demethylase 5A, ARID domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P29375	intellectual disability pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Profound Mental Retardation tuberculosis Alzheimer disease autism spectrum disorder glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis ulcerative colitis astrocytic tumor intellectual disability pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Profound Mental Retardation tuberculosis Alzheimer disease autism spectrum disorder glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease psoriasis ulcerative colitis astrocytic tumor breast cancer hepatocellular carcinoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor rheumatoid arthritis atypical teratoid rhabdoid tumor dermatomyositis malignant glioma pancreatic ductal adenocarcinoma

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.