NPASS Natural Product

Natural Product: NPC125659

Natural Product ID:	NPC125659
Common Name:	Tubercidin
IUPAC Name:	(2R,3R,4S,5R)-2-(4-aminopyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)oxolane-3,4-diol
Synonyms:	Tubercidin
Molecular Formula:	C11H14N4O4
Standard InCHIKey:	HDZZVAMISRMYHH-KCGFPETGSA-N
Standard InCHI:	InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1
Canonical SMILES:	OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc2c1ncnc2N
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO10847	Randia longiflora	Species	Rubiaceae	Eukaryota	UNPD*
NPO12856	Kadsura induta	Species	Schisandraceae	Eukaryota	UNPD*
NPO12969	Phyllosticta hydrangeae	Species	Phyllostictaceae	Eukaryota	UNPD*
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	StreptomeDB*
NPO2221	Lophozia lycopodioides	Species	Scapaniaceae	Eukaryota	UNPD*
NPO408	Garcinia dioica	Species	Clusiaceae	Eukaryota	UNPD*
NPO6258	Streptomyces tubercidicus	Species	Streptomycetaceae	Bacteria	StreptomeDB*
NPO7585	Narvalina domingensis	Species	Asteraceae	Eukaryota	UNPD*

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Biological Activity

Activity Type	# Activity
AC50	7
EC50	11
GI50	8
IC50	25
Kd	2
Ki	2
MIC	70
Others	33
Potency	32

Activity Type	# Activity
Cell Line	60
Individual Protein	27
Organism	71
Others	32

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT10	Individual Protein	Geminin	Homo sapiens	Potency		517.4	nM	PubChem BioAssay data set
NPT10	Individual Protein	Geminin	Homo sapiens	Potency		651.3	nM	PubChem BioAssay data set
NPT101	Individual Protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency		1584.9	nM	PubChem BioAssay data set
NPT1048	Organism	Poliovirus	Human enterovirus C	IC50	=	30	nM	20964406
NPT1049	Organism	Measles virus	Measles virus	MIC50	=	0.3	ug/ml	3820218
NPT11	Individual Protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency		25118.9	nM	PubChem BioAssay data set
NPT1106	Organism	Human poliovirus 1	Human poliovirus 1	MIC	=	0.007	ug/ml	6699874
NPT1106	Organism	Human poliovirus 1	Human poliovirus 1	MIC50	=	0.02	ug/ml	3820218
NPT1106	Organism	Human poliovirus 1	Human poliovirus 1	MIC	=	0.2	ug/ml	1335077
NPT1141	Organism	Human herpesvirus 2	Human herpesvirus 2	MIC	=	0.2	ug/ml	6699874

Showing 1 to 10 of 171 entries

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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 NPC125659 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	258
0.1-0.2	7435
0.2-0.3	17813
0.3-0.4	2820
0.4-0.5	1922
0.5-0.6	531
0.6-0.7	75
0.7-0.8	32
0.8-0.85	0
0.85-0.9	0
0.9-0.95	2
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.56	Remote Similarity	NPC233936
0.5602	Remote Similarity	NPC84268
0.5615	Remote Similarity	NPC469975
0.5625	Remote Similarity	NPC471322
0.5625	Remote Similarity	NPC469813

Showing 1 to 5 of 148 entries

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Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC125659 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	133
0.1-0.2	915
0.2-0.3	2338
0.3-0.4	2769
0.4-0.5	1781
0.5-0.6	1077
0.6-0.7	116
0.7-0.8	29
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5856	Remote Similarity	NPD5567	Approved
0.586	Remote Similarity	NPD1709	Phase 1
0.586	Remote Similarity	NPD4074	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD2445	Approved
0.5862	Remote Similarity	NPD2446	Approved

Showing 1 to 5 of 200 entries

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Structure

External Identifiers

PubChem CID	6245
ChEMBL	CHEMBL267099
ZINC

Physicochemical Properties

Molecular Weight:	266.10
ALogP:	-2.2791
MLogP:	1.79
XLogP:	-1.263
# Rotatable Bonds:	6
Polar Surface Area:	126.65
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	19

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