NPASS Natural Product

Natural Product: NPC152424

Natural Product ID:	NPC152424
Common Name:	5-Methoxypodophyllotoxin-4-Beta-D-Glucoside
IUPAC Name:	(5R,5aR,8aR,9R)-5-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-9-(3,4,5-trimethoxyphenyl)-5a,6,8a,9-tetrahydro-5H-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one
Synonyms:
Molecular Formula:	C28H32O13
Standard InCHIKey:	NXVJTGLCCSFGAT-QNDDJFOYSA-N
Standard InCHI:	InChI=1S/C28H32O13/c1-34-17-4-11(5-18(35-2)26(17)36-3)20-12-6-15-16(39-10-38-15)7-13(12)25(14-9-37-27(33)21(14)20)41-28-24(32)23(31)22(30)19(8-29)40-28/h4-7,14,19-25,28-32H,8-10H2,1-3H3/t14-,19+,20+,21-,22+,23-,24+,25-,28-/m0/s1
Canonical SMILES:	OC[C@H]1O[C@@H](O[C@@H]2[C@H]3COC(=O)[C@@H]3[C@@H](c3c2cc2OCOc2c3)c2cc(OC)c(c(c2)OC)OC)[C@@H]([C@H]([C@@H]1O)O)O
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Reference
NPO10903	Sinopodophyllum hexandrum	Species	Berberidaceae	Eukaryota		UNPD*
NPO11148	Antigonon leptopus	Species	Polygonaceae	Eukaryota		UNPD*
NPO11163	Methylobacterium organophilum	Species	Methylobacteriaceae	Bacteria		UNPD*
NPO11337	Machilus pseudolongifolia	Species	Lauraceae	Eukaryota		UNPD*
NPO11417	Gesneria cardinalis	Species	Crambidae	Eukaryota		UNPD*
NPO12821	Geigeria ornativa	Species	Asteraceae	Eukaryota		UNPD*
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	roots and rhizomes	PMID[21570846]
NPO207	Tephrosia maxima	Species	Geometridae	Eukaryota		UNPD*
NPO23871	Dysosmae verspiellis rhixoma et radix	NA	NA	NA		TCMSP*
NPO26353	Thuridilla hopei	Species	Placobranchidae	Eukaryota		UNPD*

Showing 1 to 10 of 19 entries

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Biological Activity

Activity Type	# Activity
ED50	2
IC50	4

Activity Type	# Activity
Cell Line	5
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	ED50	=	21.8	ug/ml	1602298
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	6650	nM	21570846
NPT2	Others	Unspecified		ED50	=	30	ug/ml	1602298
NPT3950	Cell Line	GLC4 cell line		IC50	=	10000	nM	7783142
NPT3950	Cell Line	GLC4 cell line		IC50	=	58000	nM	7783142
NPT91	Cell Line	KB	Homo sapiens	IC50	=	9250	nM	21570846

Showing 1 to 6 of 6 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 NPC152424 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	272
0.1-0.2	1014
0.2-0.3	2153
0.3-0.4	3897
0.4-0.5	6781
0.5-0.6	5420
0.6-0.7	4685
0.7-0.8	5772
0.8-0.85	700
0.85-0.9	157
0.9-0.95	23
0.95-1	15

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Similarity Score	Similarity Level	Natural Product ID
0.8491	Intermediate Similarity	NPC472709
0.8491	Intermediate Similarity	NPC472710
0.8491	Intermediate Similarity	NPC238140
0.8494	Intermediate Similarity	NPC475738
0.8497	Intermediate Similarity	NPC156376

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 NPC152424 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	267
0.1-0.2	797
0.2-0.3	1562
0.3-0.4	2638
0.4-0.5	2091
0.5-0.6	1138
0.6-0.7	518
0.7-0.8	135
0.8-0.85	5
0.85-0.9	3
0.9-0.95	3
0.95-1	4

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6851	Remote Similarity	NPD3051	Approved
0.6855	Remote Similarity	NPD2983	Phase 2
0.6855	Remote Similarity	NPD2982	Phase 2
0.6856	Remote Similarity	NPD7700	Phase 2
0.6856	Remote Similarity	NPD7699	Phase 2

Showing 1 to 5 of 200 entries

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Structure

CID152424 OpenBabel06191715522D 41 46 0 0 1 0 0 0 0 0999 V2000 6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8060 2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5296 -3.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 1.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 2.5827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5241 -2.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1229 -2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 34 1 0 0 0 0 2 35 1 0 0 0 0 3 36 1 0 0 0 0 4 11 2 0 0 0 0 4 17 1 0 0 0 0 5 11 1 0 0 0 0 5 18 2 0 0 0 0 6 12 2 0 0 0 0 6 15 1 0 0 0 0 7 13 2 0 0 0 0 7 16 1 0 0 0 0 8 29 1 0 0 0 0 9 37 1 0 0 0 0 10 38 1 0 0 0 0 10 39 1 0 0 0 0 12 13 1 0 0 0 0 12 20 1 0 0 0 0 13 25 1 0 0 0 0 14 9 1 1 0 0 0 14 21 1 0 0 0 0 14 25 1 0 0 0 0 15 16 2 0 0 0 0 15 38 1 0 0 0 0 16 39 1 0 0 0 0 17 26 2 0 0 0 0 17 34 1 0 0 0 0 18 26 1 0 0 0 0 18 35 1 0 0 0 0 19 8 1 6 0 0 0 19 22 1 0 0 0 0 19 40 1 0 0 0 0 20 11 1 6 0 0 0 20 21 1 0 0 0 0 21 27 1 6 0 0 0 22 23 1 0 0 0 0 22 30 1 1 0 0 0 23 24 1 0 0 0 0 23 31 1 6 0 0 0 24 28 1 0 0 0 0 24 32 1 1 0 0 0 25 41 1 6 0 0 0 26 36 1 0 0 0 0 27 33 2 0 0 0 0 27 37 1 0 0 0 0 28 40 1 0 0 0 0 28 41 1 6 0 0 0 M END $$$$

External Identifiers

PubChem CID	161177
ChEMBL	CHEMBL503644
ZINC

Physicochemical Properties

Molecular Weight:	576.18
ALogP:	-3.2475
MLogP:	3.11
XLogP:	0.151
# Rotatable Bonds:	14
Polar Surface Area:	171.83
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	41

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