NPASS Compound

Structure

NPC240085 OpenBabel06302215182D 27 31 0 0 1 0 0 0 0 0999 V2000 3.4726 -0.5392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6352 -0.5392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2099 -1.2759 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4733 -1.7011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 -1.2759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 -0.4253 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4732 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2098 -0.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3238 0.0001 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7425 0.7254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4732 0.8506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1879 1.2632 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7366 1.2759 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.8506 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7366 1.2758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4732 0.8505 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4732 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2985 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8858 -0.7147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7366 -0.4253 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5597 -1.2573 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1119 -1.8706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2862 -1.3461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6321 -0.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4393 -0.3975 0.0000 O 0 0 0 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 -2.1879 1.2631 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 9 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 6 0 0 0 3 8 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 1 0 0 0 6 7 1 0 0 0 0 6 26 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 7 11 1 0 0 0 0 9 10 1 6 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 26 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 27 1 1 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 20 17 1 6 0 0 0 20 21 1 0 0 0 0 20 26 1 0 0 0 0 21 22 1 1 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 26 24 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	378.17
Volume:	365.316
LogP:	0.974
LogD:	0.248
LogS:	-4.094
# Rotatable Bonds:	0
TPSA:	113.29
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.416
Synthetic Accessibility Score:	6.789
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.567
MDCK Permeability:	6.335107900667936e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.037
30% Bioavailability (F30%):	0.898

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.172
Plasma Protein Binding (PPB):	60.208824157714844%
Volume Distribution (VD):	1.155
Pgp-substrate:	42.298683166503906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.132
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.54
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.078
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.19
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.167

ADMET: Excretion

Clearance (CL):	2.856
Half-life (T1/2):	0.315

ADMET: Toxicity

hERG Blockers:	0.581
Human Hepatotoxicity (H-HT):	0.755
Drug-inuced Liver Injury (DILI):	0.076
AMES Toxicity:	0.777
Rat Oral Acute Toxicity:	0.978
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.331
Carcinogencity:	0.34
Eye Corrosion:	0.004
Eye Irritation:	0.052
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC240085

Natural Product ID:	NPC240085
*Common Name:**	WRPBKNUCLLLHGA-VCLXPVPQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WRPBKNUCLLLHGA-VCLXPVPQSA-N
Standard InCHI:	InChI=1S/C20H26O7/c1-8-9-4-5-10-19(7-9,14(8)22)16(24)26-12-6-11(21)18(2,3)13-15(23)27-17(25)20(10,12)13/h9-15,21-23H,1,4-7H2,2-3H3/t9-,10-,11+,12+,13-,14-,15-,19+,20+/m1/s1
SMILES:	C=C1[C@@H]2CC[C@@H]3[C@@](C2)([C@@H]1O)C(=O)O[C@H]1C[C@@H](C(C)(C)[C@H]2[C@H](O)OC(=O)[C@@]312)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO21139	Daphniphyllum calycinum	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19099464]
NPO19475	Isodon sculponeatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19697926]
NPO8991	Carcinus maenas	Species	Carcinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[2421673]
NPO19475	Isodon sculponeatus	Species	Lamiaceae	Eukaryota	aerial parts	Muli County, Sichuan Province, China	2011-AUG	PMID[24219809]
NPO21139	Daphniphyllum calycinum	Species	Daphniphyllaceae	Eukaryota	n.a.	leaf	n.a.	PMID[9599286]
NPO21482	Crotalaria laburnifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21482	Crotalaria laburnifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21139	Daphniphyllum calycinum	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17240	Crematogaster brevis	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20115	Melampodium argophyllum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19889	Cereus stellatus	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19763	Meloidogyne incognita	Species	Meloidogynidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21614	Urceolaria scruposa	Species	Trichodinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17508	Danae racemosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19768	Xylosalsola arbuscula	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21139	Daphniphyllum calycinum	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19475	Isodon sculponeatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20336	Arctotheca calendula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8991	Carcinus maenas	Species	Carcinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20470	Elaeagnus orientalis	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16409	Quercus pedunculata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1558	Ozothamnus obcordatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16021	Boletus bovinus	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20543	Psydrax livida	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21482	Crotalaria laburnifolia	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 NPC240085 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	265
0.1-0.2	1859
0.2-0.3	6022
0.3-0.4	10948
0.4-0.5	10187
0.5-0.6	6038
0.6-0.7	5229
0.7-0.8	1941
0.8-0.85	152
0.85-0.9	35
0.9-0.95	16
0.95-1	5

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 NPC240085 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	256
0.1-0.2	2284
0.2-0.3	3994
0.3-0.4	1713
0.4-0.5	442
0.5-0.6	246
0.6-0.7	174
0.7-0.8	41
0.8-0.85	0
0.85-0.9	0
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