NPASS Natural Product

Natural Product: NPC193536

Natural Product ID:	NPC193536
Common Name:	Spermidine
IUPAC Name:	N'-(3-aminopropyl)butane-1,4-diamine
Synonyms:	Spermidine
Molecular Formula:	C7H19N3
Standard InCHIKey:	ATHGHQPFGPMSJY-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
Canonical SMILES:	NCCCNCCCCN
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Reference
NPO29545	Capsici fructus	NA	NA	NA		TCMSP*
NPO27009	Crotalaria retusa	Species	Fabaceae	Eukaryota		TCMID*
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota		TCMID*
NPO7635	Glycine max	Species	Fabaceae	Eukaryota		TCMID*
NPO16509	Avena sativa	Species	Poaceae	Eukaryota		TCMID*
NPO21080	Solanum lycopersicum	Species	Solanaceae	Eukaryota		TCMID*
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota		TCMID*
NPO16509	Avena sativa	Species	Poaceae	Eukaryota		TCM_Taiwan*
NPO17694	Nicotiana tabacum	Species	Solanaceae	Eukaryota		TCM_Taiwan*
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	blood	Geigy Scientific Tables, 8th Rev edition. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	saliva	PMID[23857558]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	Faeces	PMID[20669995]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	cerebrospinal fluid	PMID[15745737]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	urine	PMID[3757213]
NPO20338	Mus musculus	Species	Muridae	Eukaryota		PMID[19425150]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota		TCM_Taiwan*
NPO31303	Solanum lycopersicum	Species	Solanaceae	Eukaryota		TCM_Taiwan*
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria		PMID[21988831]
NPO7635	Glycine max	Species	Fabaceae	Eukaryota		TCM_Taiwan*
NPO21260	Nectandra pichurim	Species	Lauraceae	Eukaryota		UNPD*
NPO22602	Pityrogramma tartarea	Species	Pteridaceae	Eukaryota		UNPD*
NPO20977	Capparis masaikai	Species	Capparaceae	Eukaryota		UNPD*
NPO2316	Cyanidium caldarium	Species	Cyanidiaceae	Eukaryota		UNPD*

Biological Activity

Activity Type	# Activity
AC50	2
IC50	17
Kd	1
Ki	18
Others	10
Potency	20

Activity Type	# Activity
Cell Line	14
Individual Protein	32
Organism	3
Others	12
Protein Family	1
Uncleic Acid	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT396	Cell Line	T47D	Homo sapiens	Ki	=	4400	nM	10397506
NPT317	Uncleic Acid	Nucleic Acid		IC50	=	98000	nM	11606130
NPT2	Others	Unspecified		IC50	>	100000	nM	10197971
NPT317	Uncleic Acid	Nucleic Acid		IC50	=	105000	nM	10197971
NPT82	Cell Line	MDA-MB-231	Homo sapiens	Ki	=	113	nM	11606128
NPT2	Others	Unspecified		IC50	>	100000	nM	9397169
NPT317	Uncleic Acid	Nucleic Acid		IC50	=	175000	nM	9397169
NPT1881	Uncleic Acid	Calf thymus DNA	Bos taurus	IC50	=	130000	nM	1875339
NPT317	Uncleic Acid	Nucleic Acid		IC50	=	110000	nM	1875339
NPT317	Uncleic Acid	Nucleic Acid		IC50	=	300000	nM	1875339
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	1500000	nM	1875339
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	100000	nM	1875339
NPT137	Cell Line	L1210	Mus musculus	IC50	>	100000	nM	9154970
NPT610	Others	Molecular identity unknown		Ki	=	2200	nM	9154970
NPT4102	Protein Family	Phosphodiesterase 1	Bos taurus	IC50	>	500000	nM	16392808
NPT4103	Cell Line	CHO-MG	Cricetulus griseus	IC50	>	100000	nM	16392808
NPT2	Others	Unspecified		Inhibition	=	4.8	%	18163550
NPT2	Others	Unspecified		Activity	=	5.52	%	18281932
NPT2	Others	Unspecified		Activity	=	6.07	%	18281932
NPT2	Others	Unspecified		Activity	=	58.16	%	18281932
NPT137	Cell Line	L1210	Mus musculus	IC50	>	100000	nM	18558490
NPT1161	Cell Line	CHO	Cricetulus griseus	IC50	>	100000	nM	18558490
NPT947	Individual Protein	Carbonic anhydrase I	Homo sapiens	Ki	=	1400	nM	20590092
NPT233	Individual Protein	Carbonic anhydrase II	Homo sapiens	Ki	=	1110	nM	20590092
NPT1146	Individual Protein	Carbonic anhydrase III	Homo sapiens	Ki	=	11500	nM	20590092
NPT1062	Individual Protein	Carbonic anhydrase IV	Homo sapiens	Ki	=	112	nM	20590092
NPT1143	Individual Protein	Carbonic anhydrase VA	Homo sapiens	Ki	=	1220	nM	20590092
NPT1144	Individual Protein	Carbonic anhydrase VB	Homo sapiens	Ki	=	1440	nM	20590092
NPT1063	Individual Protein	Carbonic anhydrase VI	Homo sapiens	Ki	=	1410	nM	20590092
NPT955	Individual Protein	Carbonic anhydrase VII	Homo sapiens	Ki	=	1230	nM	20590092
NPT948	Individual Protein	Carbonic anhydrase IX	Homo sapiens	Ki	=	1370	nM	20590092
NPT949	Individual Protein	Carbonic anhydrase XII	Homo sapiens	Ki	=	44100	nM	20590092
NPT1061	Individual Protein	Carbonic anhydrase XIII	Mus musculus	Ki	=	11600	nM	20590092
NPT954	Individual Protein	Carbonic anhydrase XIV	Homo sapiens	Ki	=	1000	nM	20590092
NPT1147	Individual Protein	Carbonic anhydrase 15	Mus musculus	Ki	=	10000	nM	20590092
NPT2	Others	Unspecified		Potency	=	6309.6	nM	PubChem BioAssay data set
NPT210	Individual Protein	Thyroid stimulating hormone receptor	Homo sapiens	Potency	=	31622.8	nM	PubChem BioAssay data set
NPT940	Individual Protein	Serine/threonine-protein kinase mTOR	Homo sapiens	Potency	=	26121.6	nM	PubChem BioAssay data set
NPT792	Individual Protein	Arachidonate 15-lipoxygenase	Homo sapiens	Potency	=	12589.3	nM	PubChem BioAssay data set
NPT940	Individual Protein	Serine/threonine-protein kinase mTOR	Homo sapiens	Potency	=	23280.9	nM	PubChem BioAssay data set
NPT96	Individual Protein	Thrombopoietin	Homo sapiens	Potency	=	6309.6	nM	PubChem BioAssay data set
NPT95	Individual Protein	Muscarinic acetylcholine receptor M1	Rattus norvegicus	Potency	=	8912.5	nM	PubChem BioAssay data set
NPT212	Individual Protein	Cytochrome P450 2C9	Homo sapiens	Potency	=	12589.3	nM	PubChem BioAssay data set
NPT443	Individual Protein	Histone acetyltransferase GCN5	Homo sapiens	Potency		39810.7	nM	PubChem BioAssay data set
NPT5	Individual Protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency		10621.3	nM	PubChem BioAssay data set
NPT1139	Individual Protein	Arachidonate 15-lipoxygenase, type II	Homo sapiens	Potency		12589.3	nM	PubChem BioAssay data set
NPT1139	Individual Protein	Arachidonate 15-lipoxygenase, type II	Homo sapiens	Potency		5011.9	nM	PubChem BioAssay data set
NPT64	Individual Protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency		2058.8	nM	PubChem BioAssay data set
NPT208	Individual Protein	Cytochrome P450 1A2	Homo sapiens	AC50	=	31622.78	nM	PubChem BioAssay data set
NPT212	Individual Protein	Cytochrome P450 2C9	Homo sapiens	AC50	=	12589.25	nM	PubChem BioAssay data set
NPT7	Individual Protein	Thioredoxin reductase 1, cytoplasmic	Rattus norvegicus	Potency		398.1	nM	PubChem BioAssay data set
NPT71	Cell Line	HEK293	Homo sapiens	Potency		6510.4	nM	PubChem BioAssay data set
NPT90	Cell Line	DU-145	Homo sapiens	Activity	=	89	%	21639123
NPT90	Cell Line	DU-145	Homo sapiens	Activity	<	0.005	nmol	21639123
NPT90	Cell Line	DU-145	Homo sapiens	Activity	=	0.126	nmol	21639123
NPT2	Others	Unspecified		Potency		0.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency		1.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency		8407.1	nM	PubChem BioAssay data set
NPT49	Individual Protein	DNA-(apurinic or apyrimidinic site) lyase	Homo sapiens	Potency		12589.3	nM	PubChem BioAssay data set
NPT5095	Individual Protein	Ornithine decarboxylase	Bos taurus	Ki	=	3000000	nM	619149
NPT4628	Individual Protein	Ornithine decarboxylase	Rattus norvegicus	Ki	=	2700000	nM	619149
NPT2	Others	Unspecified		Kd	=	700000	nM	619149
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC99	>	512	ug/ml	26964758
NPT1548	Organism	Pseudomonas aeruginosa PAO1	Pseudomonas aeruginosa PAO1	MIC99	>	512	ug/ml	26964758
NPT19	Organism	Escherichia coli	Escherichia coli	MIC99	>	512	ug/ml	26964758

Similar Natural Products in NPASS

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC193536 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	20600
0.1-0.2	8837
0.2-0.3	975
0.3-0.4	373
0.4-0.5	69
0.5-0.6	9
0.6-0.7	12
0.7-0.8	9
0.8-0.85	0
0.85-0.9	2
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9615	High Similarity	NPC27675
0.9286	High Similarity	NPC95589
0.9259	High Similarity	NPC152949
0.8966	High Similarity	NPC320889
0.8571	High Similarity	NPC270175
0.7931	Intermediate Similarity	NPC232311
0.7879	Intermediate Similarity	NPC74599
0.7429	Intermediate Similarity	NPC326791
0.7419	Intermediate Similarity	NPC21157
0.7407	Intermediate Similarity	NPC119368
0.7308	Intermediate Similarity	NPC309330
0.7308	Intermediate Similarity	NPC28081
0.7222	Intermediate Similarity	NPC240230
0.7027	Intermediate Similarity	NPC321202
0.6923	Remote Similarity	NPC309715
0.6842	Remote Similarity	NPC319114
0.6786	Remote Similarity	NPC306277
0.6667	Remote Similarity	NPC27869
0.6571	Remote Similarity	NPC163099
0.6486	Remote Similarity	NPC473035
0.6486	Remote Similarity	NPC270319
0.6389	Remote Similarity	NPC203203
0.6316	Remote Similarity	NPC167301
0.6	Remote Similarity	NPC15231
0.6	Remote Similarity	NPC83032
0.6	Remote Similarity	NPC125872
0.5758	Remote Similarity	NPC313882
0.5667	Remote Similarity	NPC318947

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC193536 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1574
0.1-0.2	6346
0.2-0.3	842
0.3-0.4	294
0.4-0.5	57
0.5-0.6	34
0.6-0.7	5
0.7-0.8	6
0.8-0.85	2
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9286	High Similarity	NPD401	Approved
0.8333	Intermediate Similarity	NPD1156	Clinical (unspecified phase)
0.8065	Intermediate Similarity	NPD2276	Clinical (unspecified phase)
0.7586	Intermediate Similarity	NPD9064	Approved
0.7586	Intermediate Similarity	NPD9063	Approved
0.7429	Intermediate Similarity	NPD2707	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD9465	Approved
0.7308	Intermediate Similarity	NPD8560	Clinical (unspecified phase)
0.7027	Intermediate Similarity	NPD2273	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD8544	Approved
0.6579	Remote Similarity	NPD1463	Clinical (unspecified phase)
0.641	Remote Similarity	NPD9227	Discontinued
0.6216	Remote Similarity	NPD9059	Approved
0.6154	Remote Similarity	NPD8822	Approved
0.5926	Remote Similarity	NPD7383	Phase 3
0.5854	Remote Similarity	NPD9458	Approved
0.5814	Remote Similarity	NPD1154	Phase 3
0.5625	Remote Similarity	NPD8791	Clinical (unspecified phase)

Structure

External Identifiers

PubChem CID	1102
ChEMBL	CHEMBL19612
ZINC

Physicochemical Properties

Molecular Weight:	145.16
ALogP:	-2.7378
MLogP:	1.9
XLogP:	-0.654
# Rotatable Bonds:	9
Polar Surface Area:	64.07
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	10

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