MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
1AXC	2.6	HUMAN PCNA
2ZVV	2.0	Crystal structure of Proliferating cellular nuclear antigen 1 and Short peptide from human P21
2ZVW	2.5	Crystal structure of Proliferating cell nuclear antigen 2 and Short peptide from human P21
4RJF	2.0072	Crystal structure of the human sliding clamp at 2.0 angstrom resolution
5E0U	1.93	Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
6CBI	2.75	PCNA in complex with inhibitor
6CEJ		Solution structure of a 14mer fragment of the p21 protein
6CIV		Lactam cyclised mimetic of a fragment of p21
6CIX		Lactam cyclised mimetic of a fragment of p21
6P8H	3.19	Crystal structure of CDK4 in complex with CyclinD1 and P21
7KQ0	2.4	PCNA bound to peptide mimetic
7KQ1	3.3	PCNA bound to truncated peptide mimetic

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006974	DNA damage response
Biological Process	GO:0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
Biological Process	GO:0006978	DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
Biological Process	GO:0000082	G1/S transition of mitotic cell cycle
Biological Process	GO:0007265	Ras protein signal transduction
Biological Process	GO:0071493	cellular response to UV-B
Biological Process	GO:0034198	cellular response to amino acid starvation
Biological Process	GO:0031668	cellular response to extracellular stimulus
Biological Process	GO:0071480	cellular response to gamma radiation
Biological Process	GO:0071479	cellular response to ionizing radiation
Biological Process	GO:0090398	cellular senescence
Biological Process	GO:0007507	heart development
Biological Process	GO:0097193	intrinsic apoptotic signaling pathway
Biological Process	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
Biological Process	GO:0030216	keratinocyte differentiation
Biological Process	GO:0043616	keratinocyte proliferation
Biological Process	GO:0007095	mitotic G2 DNA damage checkpoint signaling
Biological Process	GO:2000279	negative regulation of DNA biosynthetic process
Biological Process	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle
Biological Process	GO:1905179	negative regulation of cardiac muscle tissue regeneration
Biological Process	GO:0030308	negative regulation of cell growth
Biological Process	GO:0008285	negative regulation of cell population proliferation
Biological Process	GO:1904030	negative regulation of cyclin-dependent protein kinase activity
Biological Process	GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity
Biological Process	GO:0010629	negative regulation of gene expression
Biological Process	GO:0042326	negative regulation of phosphorylation
Biological Process	GO:0032091	negative regulation of protein binding
Biological Process	GO:0001933	negative regulation of protein phosphorylation
Biological Process	GO:1904706	negative regulation of vascular associated smooth muscle cell proliferation
Biological Process	GO:0090402	oncogene-induced cell senescence
Biological Process	GO:0030890	positive regulation of B cell proliferation
Biological Process	GO:0048146	positive regulation of fibroblast proliferation
Biological Process	GO:0043068	positive regulation of programmed cell death
Biological Process	GO:0045860	positive regulation of protein kinase activity
Biological Process	GO:0001934	positive regulation of protein phosphorylation
Biological Process	GO:2000379	positive regulation of reactive oxygen species metabolic process
Biological Process	GO:0006606	protein import into nucleus
Biological Process	GO:2000045	regulation of G1/S transition of mitotic cell cycle
Biological Process	GO:0010389	regulation of G2/M transition of mitotic cell cycle
Biological Process	GO:0051726	regulation of cell cycle
Biological Process	GO:1902806	regulation of cell cycle G1/S phase transition
Biological Process	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity
Biological Process	GO:0090399	replicative senescence
Biological Process	GO:0090400	stress-induced premature senescence
Biological Process	GO:0042246	tissue regeneration
Biological Process	GO:0042060	wound healing
Molecular Function	GO:0030332	cyclin binding
Molecular Function	GO:0019912	cyclin-dependent protein kinase activating kinase activity
Molecular Function	GO:0004861	cyclin-dependent protein serine/threonine kinase inhibitor activity
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:0140677	molecular function activator activity
Molecular Function	GO:0140678	molecular function inhibitor activity
Molecular Function	GO:0019901	protein kinase binding
Molecular Function	GO:0004860	protein kinase inhibitor activity
Molecular Function	GO:0140311	protein sequestering activity
Molecular Function	GO:0044877	protein-containing complex binding
Molecular Function	GO:0031625	ubiquitin protein ligase binding
Cellular Component	GO:0070557	PCNA-p21 complex
Cellular Component	GO:0000307	cyclin-dependent protein kinase holoenzyme complex
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0016604	nuclear body
Cellular Component	GO:0005730	nucleolus
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0032991	protein-containing complex

InterPro / Pfam

InterPro	InterPro name
IPR003175	Cyclin-dependent kinase inhibitor domain
IPR029841	Cyclin-dependent kinase inhibitor 1
IPR044898	Cyclin-dependent kinase inhibitor domain superfamily

Pfam	Pfam name
PF02234	Cyclin-dependent kinase inhibitor

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-187577	SCF(Skp2)-mediated degradation of p27/p21	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-198323	AKT phosphorylates targets in the cytosol	Leaf	R-HSA-162582	Signal Transduction
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)	Leaf	R-HSA-8953897	Cellular responses to stimuli
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence	Internal node	R-HSA-8953897	Cellular responses to stimuli
R-HSA-5674400	Constitutive Signaling by AKT1 E17K in Cancer	Leaf	R-HSA-1643685	Disease
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	Leaf	R-HSA-168256	Immune System
R-HSA-6804116	TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-69202	Cyclin E associated events during G1/S transition	Internal node	R-HSA-1640170	Cell Cycle
R-HSA-69231	Cyclin D associated events in G1	Internal node	R-HSA-1640170	Cell Cycle
R-HSA-69563	p53-Dependent G1 DNA Damage Response	Internal node	R-HSA-1640170	Cell Cycle
R-HSA-69656	Cyclin A:Cdk2-associated events at S phase entry	Internal node	R-HSA-1640170	Cell Cycle
R-HSA-69895	Transcriptional activation of cell cycle inhibitor p21	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-8852276	The role of GTSE1 in G2/M progression after G2 checkpoint	Leaf	R-HSA-1640170	Cell Cycle
R-HSA-8866911	TFAP2 (AP-2) family regulates transcription of cell cycle factors	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8878166	Transcriptional regulation by RUNX2	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-8941855	RUNX3 regulates CDKN1A transcription	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8951664	Neddylation	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-9616222	Transcriptional regulation of granulopoiesis	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-9617828	FOXO-mediated transcription of cell cycle genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9661069	Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)	Leaf	R-HSA-1643685	Disease
R-HSA-9702518	STAT5 activation downstream of FLT3 ITD mutants	Leaf	R-HSA-1643685	Disease
R-HSA-9703465	Signaling by FLT3 fusion proteins	Leaf	R-HSA-1643685	Disease
R-HSA-9755511	KEAP1-NFE2L2 pathway	Internal node	R-HSA-8953897	Cellular responses to stimuli

Subcellular location

Location	ECO term	Pubmed
Cytoplasm	ECO:0000269	PubMed:11463845
Nucleus	ECO:0000269	PubMed:11463845
Nucleus	ECO:0000269	PubMed:23213251

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000141	Amenorrhea
HP:0000169	Gingival fibromatosis
HP:0000716	Depression
HP:0000736	Short attention span
HP:0000787	Nephrolithiasis
HP:0000802	Impotence
HP:0000822	Hypertension
HP:0000845	Elevated circulating growth hormone concentration
HP:0000849	Adrenocortical abnormality
HP:0000853	Goiter
HP:0001012	Multiple lipomas
HP:0001254	Lethargy
HP:0001259	Coma
HP:0001289	Confusion
HP:0001293	Cranial nerve compression
HP:0001579	Primary hypercortisolism
HP:0001824	Weight loss
HP:0001944	Dehydration
HP:0002013	Vomiting
HP:0002014	Diarrhea
HP:0002018	Nausea
HP:0002019	Constipation
HP:0002020	Gastroesophageal reflux
HP:0002027	Abdominal pain
HP:0002039	Anorexia
HP:0002044	Zollinger-Ellison syndrome
HP:0002150	Hypercalciuria
HP:0002248	Hematemesis
HP:0002249	Melena
HP:0002315	Headache
HP:0002588	Duodenal ulcer
HP:0002659	Increased susceptibility to fractures
HP:0002666	Pheochromocytoma
HP:0002797	Osteolysis
HP:0002858	Meningioma
HP:0002888	Ependymoma
HP:0002890	Thyroid carcinoma
HP:0002893	Pituitary adenoma
HP:0002894	Neoplasm of the pancreas
HP:0003072	Hypercalcemia
HP:0003118	Increased circulating cortisol level
HP:0003144	Increased serum serotonin
HP:0003528	Elevated calcitonin
HP:0004349	Reduced bone mineral density
HP:0004398	Peptic ulcer
HP:0005605	Large cafe-au-lait macules with irregular margins
HP:0006723	Intestinal carcinoid
HP:0006744	Adrenocortical carcinoma
HP:0006767	Pituitary prolactin cell adenoma
HP:0006780	Parathyroid carcinoma
HP:0007449	Confetti-like hypopigmented macules
HP:0008200	Primary hyperparathyroidism
HP:0008208	Parathyroid hyperplasia
HP:0008291	Pituitary corticotropic cell adenoma
HP:0010615	Angiofibromas
HP:0011151	Atypical absence status epilepticus
HP:0011407	Proportionate tall stature
HP:0011759	Pituitary gonadotropic cell adenoma
HP:0011760	Pituitary growth hormone cell adenoma
HP:0011761	Pituitary null cell adenoma
HP:0011762	Pituitary thyrotropic cell adenoma
HP:0012197	Insulinoma
HP:0012232	Shortened QT interval
HP:0030404	Glucagonoma
HP:0030405	Pancreatic endocrine tumor
HP:0030445	Pulmonary carcinoid tumor
HP:0031058	Impairment of activities of daily living
HP:0032044	Decreased vigilance
HP:0040085	Abnormal circulating aldosterone
HP:0040306	Decreased male libido
HP:0100522	Thymoma
HP:0100570	Carcinoid tumor
HP:0100829	Galactorrhea
HP:0500167	Hypergastrinemia

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Medium	Supported
adrenal gland	glandular cells	Medium	Supported
appendix	glandular cells	Medium	Supported
bone marrow	hematopoietic cells	Low	Supported
breast	glandular cells	Low	Supported
bronchus	ciliated cells (cell body)	Medium	Supported
cervix	squamous epithelial cells	High	Supported
colon	glandular cells	Medium	Supported
duodenum	glandular cells	Medium	Supported
endometrium 2	glandular cells	Medium	Supported
epididymis	glandular cells	Medium	Supported
esophagus	squamous epithelial cells	Medium	Supported
fallopian tube	ciliated cells (cell body)	Medium	Supported
gallbladder	glandular cells	Low	Supported
kidney	cells in glomeruli	Low	Supported
kidney	cells in tubules	Low	Supported
liver	cholangiocytes	Medium	Supported
liver	hepatocytes	Low	Supported
lung	macrophages	Medium	Supported
lymph node	germinal center cells	Low	Supported
lymph node	non-germinal center cells	Low	Supported
oral mucosa	squamous epithelial cells	Medium	Supported
pancreas	exocrine glandular cells	Low	Supported
pancreas	pancreatic endocrine cells	Medium	Supported
parathyroid gland	glandular cells	Low	Supported
placenta	cytotrophoblasts	High	Supported
placenta	hofbauer cells	High	Supported
prostate	glandular cells	Low	Supported
rectum	glandular cells	Medium	Supported
seminal vesicle	glandular cells	Low	Supported
skin 1	cells in spinous layer	Low	Supported
skin 1	lymphocytes	Low	Supported
skin 2	cells in spinous layer	Medium	Supported
skin 2	endothelial cells	High	Supported
skin 2	fibrohistiocytic cells	High	Supported
small intestine	glandular cells	Medium	Supported
spleen	cells in red pulp	Low	Supported
stomach 1	glandular cells	Low	Supported
stomach 2	glandular cells	Low	Supported
testis	Leydig cells	Low	Supported
testis	elongated or late spermatids	Low	Supported
testis	preleptotene spermatocytes	Low	Supported
testis	spermatogonia cells	Low	Supported
thyroid gland	glandular cells	Medium	Supported
tonsil	non-germinal center cells	Low	Supported
tonsil	squamous epithelial cells	Medium	Supported
urinary bladder	urothelial cells	Medium	Supported
vagina	squamous epithelial cells	High	Supported

Summary of P38936

Gene: CDKN1A, CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1
Protein: Cyclin-dependent kinase inhibitor 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P38936

Gene: CDKN1A, CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1 Protein: Cyclin-dependent kinase inhibitor 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: CDKN1A, CAP20, CDKN1, CIP1, MDA6, PIC1, SDI1, WAF1
Protein: Cyclin-dependent kinase inhibitor 1