NPASS Natural Product

Natural Product: NPC273410

Natural Product ID:	NPC273410
Common Name:	(20S)-Protopanaxadiol
IUPAC Name:	(3S,5R,8R,9R,10R,12R,13R,14R,17S)-17-[(2S)-2-hydroxy-6-methylhept-5-en-2-yl]-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,12-diol
Synonyms:	20(S)-Protopanaxadiol
Molecular Formula:	C30H52O3
Standard InCHIKey:	PYXFVCFISTUSOO-HKUCOEKDSA-N
Standard InCHI:	InChI=1S/C30H52O3/c1-19(2)10-9-14-30(8,33)20-11-16-29(7)25(20)21(31)18-23-27(5)15-13-24(32)26(3,4)22(27)12-17-28(23,29)6/h10,20-25,31-33H,9,11-18H2,1-8H3/t20-,21+,22-,23+,24-,25-,27-,28+,29+,30-/m0/s1
Canonical SMILES:	CC(=CCC[C@@]([C@H]1CC[C@@]2([C@@H]1[C@H](O)C[C@H]1[C@@]2(C)CC[C@@H]2[C@]1(C)CC[C@@H](C2(C)C)O)C)(O)C)C
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	UNPD*
NPO11248	Tachigalia paniculata	NA	NA	NA	UNPD*
NPO11488	Alstonia muelleriana	Species	Apocynaceae	Eukaryota	UNPD*
NPO11642	Dacrydium cupressinum	Species	Podocarpaceae	Eukaryota	UNPD*
NPO11990	Coleostephus myconis	Species	Asteraceae	Eukaryota	UNPD*
NPO12001	Saccharomyces pastori	Species	Saccharomycetaceae	Eukaryota	UNPD*
NPO12684	Trigonella grandiflora	Species	Fabaceae	Eukaryota	UNPD*
NPO12934	Gynostemma pentaphyllum	Species	Cucurbitaceae	Eukaryota	UNPD*
NPO13166	Nicotiana undulata	Species	Solanaceae	Eukaryota	UNPD*
NPO13568	Hypoxylon rubiginosum	Species	Xylariaceae	Eukaryota	UNPD*

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Biological Activity

Activity Type	# Activity
EC50	1
IC50	15
MIC	6
Others	12

Activity Type	# Activity
Cell Line	22
Individual Protein	3
Organism	6
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	16	ug/ml	23994872
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	27060	nM	21216145
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	15530	nM	26420067
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	32	ug/ml	23994872
NPT1664	Individual Protein	Squalene synthetase	Rattus norvegicus	Inhibition	=	20	%	10.1016/S0960-894X(97)00139-X
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	23600	nM	23177789
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	128	ug/ml	23994872
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	64	ug/ml	23994872
NPT2	Others	Unspecified		Activity	=	51.01	%	17261067
NPT2	Others	Unspecified		IC50	=	36740	nM	22342101

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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 NPC273410 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	96
0.1-0.2	902
0.2-0.3	3640
0.3-0.4	11041
0.4-0.5	6188
0.5-0.6	3551
0.6-0.7	3493
0.7-0.8	1507
0.8-0.85	206
0.85-0.9	215
0.9-0.95	39
0.95-1	11

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Similarity Score	Similarity Level	Natural Product ID
0.859	High Similarity	NPC18603
0.859	High Similarity	NPC307965
0.859	High Similarity	NPC253807
0.859	High Similarity	NPC98386
0.859	High Similarity	NPC76931

Showing 1 to 5 of 200 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 NPC273410 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	128
0.1-0.2	1342
0.2-0.3	4150
0.3-0.4	2446
0.4-0.5	618
0.5-0.6	178
0.6-0.7	176
0.7-0.8	102
0.8-0.85	15
0.85-0.9	5
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6627	Remote Similarity	NPD4789	Approved
0.6629	Remote Similarity	NPD4139	Approved
0.6629	Remote Similarity	NPD4692	Approved
0.663	Remote Similarity	NPD6098	Approved
0.6632	Remote Similarity	NPD5284	Approved

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Structure

CID273410 OpenBabel06191716082D 33 36 0 0 1 0 0 0 0 0999 V2000 4.6076 0.7278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1875 -0.0920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2824 -2.8774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1328 -2.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4622 0.5083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8803 -1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0009 2.8410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2408 1.5477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1875 1.5477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6403 0.9471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6415 -1.8953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1026 -0.4738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7675 2.3676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2824 0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6403 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8208 -1.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6415 0.9471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6609 0.7278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8208 1.4209 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8207 1.4209 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4622 -1.4215 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6415 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1026 -1.4214 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.9471 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2824 -1.8953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4622 -0.4738 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8207 -0.4738 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8208 2.3676 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8207 2.3937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9450 -1.9077 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8208 3.3143 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 1 0 0 0 0 2 19 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 6 28 1 0 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 19 2 0 0 0 0 11 16 1 0 0 0 0 11 20 1 0 0 0 0 12 17 1 0 0 0 0 12 22 1 0 0 0 0 13 15 1 0 0 0 0 13 24 1 0 0 0 0 14 30 1 0 0 0 0 15 27 1 0 0 0 0 16 29 1 0 0 0 0 17 28 1 0 0 0 0 18 21 1 0 0 0 0 18 23 1 0 0 0 0 20 25 1 0 0 0 0 20 30 1 1 0 0 0 21 25 1 0 0 0 0 21 31 1 1 0 0 0 22 26 1 0 0 0 0 22 27 1 1 0 0 0 23 27 1 1 0 0 0 23 28 1 0 0 0 0 24 26 1 0 0 0 0 24 32 1 1 0 0 0 25 29 1 6 0 0 0 27 5 1 1 0 0 0 28 29 1 6 0 0 0 29 7 1 6 0 0 0 30 8 1 6 0 0 0 30 33 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	11213350
ChEMBL	CHEMBL375563
ZINC

Physicochemical Properties

Molecular Weight:	460.39
ALogP:	2.5349
MLogP:	4.43
XLogP:	7.963
# Rotatable Bonds:	15
Polar Surface Area:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	33

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