NPASS Compound

Structure

CID241600 OpenBabel06191716042D 50 53 0 0 1 0 0 0 0 0999 V2000 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.4536 -2.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.9670 3.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.4670 -1.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9670 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 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 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 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 -6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9670 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9670 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1883 -1.2601 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 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4754 -2.4190 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 -9.4670 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8793 -0.3090 0.0000 C 0 0 2 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 -10.9670 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.9670 -0.3660 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 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 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 -8.4670 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.4670 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 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 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8063 -3.1622 0.0000 O 0 0 0 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 0.0000 -3.0000 0.0000 O 0 0 0 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 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.4670 2.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.4670 -1.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.4670 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1664 -1.4680 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8793 1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 2 0 0 0 0 2 19 1 0 0 0 0 3 42 1 0 0 0 0 4 43 1 0 0 0 0 5 44 1 0 0 0 0 6 45 1 0 0 0 0 7 8 2 0 0 0 0 7 11 1 0 0 0 0 8 20 1 0 0 0 0 9 10 1 0 0 0 0 9 18 1 0 0 0 0 10 36 1 0 0 0 0 11 46 1 0 0 0 0 12 20 2 0 0 0 0 12 22 1 0 0 0 0 13 20 1 0 0 0 0 13 24 2 0 0 0 0 14 21 2 0 0 0 0 14 25 1 0 0 0 0 15 21 1 0 0 0 0 15 26 2 0 0 0 0 16 47 1 0 0 0 0 17 48 1 0 0 0 0 18 34 1 0 0 0 0 19 37 2 0 0 0 0 19 47 1 0 0 0 0 22 23 1 0 0 0 0 22 32 2 0 0 0 0 23 16 1 1 0 0 0 23 31 1 0 0 0 0 24 32 1 0 0 0 0 24 42 1 0 0 0 0 25 33 2 0 0 0 0 25 43 1 0 0 0 0 26 33 1 0 0 0 0 26 44 1 0 0 0 0 27 17 1 6 0 0 0 27 28 1 0 0 0 0 27 49 1 0 0 0 0 28 29 1 0 0 0 0 28 38 1 1 0 0 0 29 30 1 0 0 0 0 29 39 1 6 0 0 0 30 35 1 0 0 0 0 30 40 1 1 0 0 0 31 21 1 6 0 0 0 31 50 1 0 0 0 0 32 50 1 0 0 0 0 33 45 1 0 0 0 0 34 41 2 0 0 0 0 34 48 1 0 0 0 0 35 46 1 6 0 0 0 35 49 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	704.27
Volume:	685.179
LogP:	1.672
LogD:	1.739
LogS:	-4.195
# Rotatable Bonds:	18
TPSA:	198.13
# H-Bond Aceptor:	15
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.146
Synthetic Accessibility Score:	4.854
Fsp3:	0.486
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.477
MDCK Permeability:	4.010337215731852e-05
Pgp-inhibitor:	0.59
Pgp-substrate:	0.98
Human Intestinal Absorption (HIA):	0.061
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.067

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.493
Plasma Protein Binding (PPB):	47.72032165527344%
Volume Distribution (VD):	0.418
Pgp-substrate:	30.671245574951172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.712
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.658
CYP2C9-inhibitor:	0.088
CYP2C9-substrate:	0.076
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.149
CYP3A4-inhibitor:	0.231
CYP3A4-substrate:	0.831

ADMET: Excretion

Clearance (CL):	3.619
Half-life (T1/2):	0.756

ADMET: Toxicity

hERG Blockers:	0.273
Human Hepatotoxicity (H-HT):	0.302
Drug-inuced Liver Injury (DILI):	0.447
AMES Toxicity:	0.572
Rat Oral Acute Toxicity:	0.096
Maximum Recommended Daily Dose:	0.248
Skin Sensitization:	0.859
Carcinogencity:	0.194
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.016

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC241600

Natural Product ID:	NPC241600
*Common Name:**	Woorenoside Iv
IUPAC Name:	[(2R,3S,4S,5R,6R)-6-[(E)-3-[(2R,3S)-3-(acetyloxymethyl)-7-methoxy-2-(3,4,5-trimethoxyphenyl)-2,3-dihydro-1-benzofuran-5-yl]prop-2-enoxy]-3,4,5-trihydroxyoxan-2-yl]methyl 4-hydroxy-2-methylidenebutanoate
Synonyms:	Woorenoside IV
Standard InCHIKey:	NKHJLZUONNNHMW-OWLKOJIMSA-N
Standard InCHI:	InChI=1S/C35H44O15/c1-18(9-10-36)34(41)48-17-27-28(38)29(39)30(40)35(49-27)46-11-7-8-20-12-22-23(16-47-19(2)37)31(50-32(22)24(13-20)42-3)21-14-25(43-4)33(45-6)26(15-21)44-5/h7-8,12-15,23,27-31,35-36,38-40H,1,9-11,16-17H2,2-6H3/b8-7+/t23-,27-,28-,29+,30-,31+,35-/m1/s1
SMILES:	C=C(CCO)C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](OC/C=C/c2cc3[C@@H](COC(=O)C)[C@H](c4cc(c(c(c4)OC)OC)OC)Oc3c(c2)OC)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL454818
PubChem CID:	10101270
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003918] Saccharolipids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO10662	Scrippsiella trochoidea	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8021655]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21401114]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[11000020]
NPO2787	Cussonia racemosa	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14345	Androsace septentrionalis	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO742	Aloe saponaria	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11281	Euphorbia fortissima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10662	Scrippsiella trochoidea	Species	Peridiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16092	Calocephalus knappii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 18 entries

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☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
IC50	5
Others	1

Activity Type	# Activity
Cell Line	4
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	14400.0	nM	PMID[489518]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	46600.0	nM	PMID[489518]
NPT2157	Cell Line	SUP-T1	Homo sapiens	IC50	=	64800.0	nM	PMID[489518]
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	=	42.7	%	PMID[489518]
NPT2	Others	Unspecified		IC50	=	20200.0	nM	PMID[489518]
NPT2	Others	Unspecified		IC50	=	24000.0	nM	PMID[489518]

Showing 1 to 6 of 6 entries

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available 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 NPC241600 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	333
0.1-0.2	1403
0.2-0.3	3213
0.3-0.4	7614
0.4-0.5	10177
0.5-0.6	5324
0.6-0.7	6394
0.7-0.8	7036
0.8-0.85	1038
0.85-0.9	152
0.9-0.95	9
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC173726
0.96	High Similarity	NPC302610
0.9477	High Similarity	NPC228357
0.9333	High Similarity	NPC270751
0.9108	High Similarity	NPC478269

Showing 1 to 5 of 200 entries

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC241600 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	276
0.1-0.2	848
0.2-0.3	1720
0.3-0.4	2728
0.4-0.5	1897
0.5-0.6	1001
0.6-0.7	544
0.7-0.8	120
0.8-0.85	16
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8671	High Similarity	NPD37	Approved
0.8625	High Similarity	NPD4967	Phase 2
0.8625	High Similarity	NPD4965	Approved
0.8625	High Similarity	NPD4966	Approved
0.8606	High Similarity	NPD7228	Approved

Showing 1 to 5 of 200 entries

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Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data