NPASS Compound

Structure

NPC157288 OpenBabel06302215392D 31 35 0 0 1 0 0 0 0 0999 V2000 -1.6839 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 1.4583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8420 2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 0.4861 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2098 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6839 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 -0.9722 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.2098 -1.4583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3679 -1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 -2.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8938 -2.4306 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.8938 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8660 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3799 -0.6164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 -0.9722 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.0518 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3679 0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7358 -2.9167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 0.4861 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 30 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 1 0 0 0 0 5 6 1 1 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 6 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 11 29 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 26 1 0 0 0 0 14 15 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 1 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 29 30 1 0 0 0 0 30 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.39
Volume:	490.807
LogP:	6.558
LogD:	5.151
LogS:	-6.549
# Rotatable Bonds:	0
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.389
Synthetic Accessibility Score:	4.842
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.925
MDCK Permeability:	9.963438969862182e-06
Pgp-inhibitor:	0.025
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.933
30% Bioavailability (F30%):	0.869

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.774
Plasma Protein Binding (PPB):	97.8725357055664%
Volume Distribution (VD):	1.328
Pgp-substrate:	2.0210888385772705%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.547
CYP2C19-inhibitor:	0.072
CYP2C19-substrate:	0.935
CYP2C9-inhibitor:	0.106
CYP2C9-substrate:	0.311
CYP2D6-inhibitor:	0.11
CYP2D6-substrate:	0.872
CYP3A4-inhibitor:	0.252
CYP3A4-substrate:	0.444

ADMET: Excretion

Clearance (CL):	6.08
Half-life (T1/2):	0.022

ADMET: Toxicity

hERG Blockers:	0.078
Human Hepatotoxicity (H-HT):	0.128
Drug-inuced Liver Injury (DILI):	0.034
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.406
Maximum Recommended Daily Dose:	0.946
Skin Sensitization:	0.697
Carcinogencity:	0.012
Eye Corrosion:	0.169
Eye Irritation:	0.246
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC157288

Natural Product ID:	NPC157288
*Common Name:**	XWMMEBCFHUKHEX-VPUBHQHASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XWMMEBCFHUKHEX-VPUBHQHASA-N
Standard InCHI:	InChI=1S/C30H50O/c1-19-11-14-27(5)17-18-29(7)21(25(27)20(19)2)9-10-23-28(6)15-13-24(31)26(3,4)22(28)12-16-30(23,29)8/h20-25,31H,1,9-18H2,2-8H3/t20-,21?,22?,23?,24+,25?,27-,28+,29-,30-/m1/s1
SMILES:	C=C1CC[C@]2(C)CC[C@]3(C)C(CCC4[C@@]5(C)CC[C@@H](C(C)(C)C5CC[C@@]34C)O)C2[C@@H]1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5270604
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	Roots	n.a.	n.a.	PMID[14510592]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	flowers	n.a.	n.a.	PMID[16643020]
NPO30603	Saussurea lappa	n.a.	n.a.	n.a.	n.a.	root	n.a.	PMID[18409040]
NPO30603	Saussurea lappa	n.a.	n.a.	n.a.	roots	n.a.	n.a.	PMID[18579374]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23189738]
NPO30603	Saussurea lappa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[25068579]
NPO23320	Marsdenia tenacissima	Species	Apocynaceae	Eukaryota	stems	Simao County, Yunnan Province, China	2005-MAR	PMID[25215856]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[25282892]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27276091]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572418]
NPO30603	Saussurea lappa	n.a.	n.a.	n.a.	n.a.	root	n.a.	PMID[8541643]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO27772	Flos inulae	Species	Lycaenidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17782.1	Inula britannica var. chinensis	Varieties	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25814	Isodon loxothyrsa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30603	Saussurea lappa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29601	Abrus fruticulosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23795	Herba seu radix cirsii japonici	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO27772	Flos inulae	Species	Lycaenidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25890	Herba cirsii japonici	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25628	Abrus pulchellus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23320	Marsdenia tenacissima	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19689	Radix cirsii japonici	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25814	Isodon loxothyrsa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17782.1	Inula britannica var. chinensis	Varieties	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29601	Abrus fruticulosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23320	Marsdenia tenacissima	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29601	Abrus fruticulosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8881	Centipeda minima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9124	Inula japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29396	Bidens bipinnata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25628	Abrus pulchellus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC157288 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	256
0.1-0.2	2878
0.2-0.3	12960
0.3-0.4	13721
0.4-0.5	5052
0.5-0.6	4324
0.6-0.7	2683
0.7-0.8	722
0.8-0.85	49
0.85-0.9	49
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID

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 NPC157288 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	264
0.1-0.2	3123
0.2-0.3	3938
0.3-0.4	1290
0.4-0.5	250
0.5-0.6	212
0.6-0.7	66
0.7-0.8	6
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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