NPASS Compound

Structure

NPC15498 OpenBabel06302215302D 36 40 0 0 1 0 0 0 0 0999 V2000 0.0026 -2.9798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8728 -2.4763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8719 -1.4710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0008 -0.9691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8380 -1.4544 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6777 -0.9706 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5479 -1.4740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6785 -0.0015 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8397 0.4838 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8400 1.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5191 1.4528 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5194 2.4528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3594 1.9377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1994 1.4524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1992 0.4829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3589 -0.0019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5188 0.4833 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5186 -0.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0397 1.9372 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0395 0.9372 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8792 1.4519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7189 1.9367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7192 2.9068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5854 3.4064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8797 3.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8800 4.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7458 3.8921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0400 2.9073 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2000 3.3926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3597 2.9078 0.0000 C 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 -0.8371 -2.4597 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7073 -2.9631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5784 -2.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7064 -3.9685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7439 -2.9782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 36 1 0 0 0 0 4 3 1 1 0 0 0 4 5 1 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 5 32 1 6 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 17 1 0 0 0 0 9 10 1 0 0 0 0 9 31 1 0 0 0 0 10 11 1 0 0 0 0 11 17 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 30 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 28 1 0 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	496.36
Volume:	543.861
LogP:	6.027
LogD:	4.533
LogS:	-5.736
# Rotatable Bonds:	3
TPSA:	52.6
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.299
Synthetic Accessibility Score:	5.204
Fsp3:	0.812
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.966
MDCK Permeability:	1.5935645933495834e-05
Pgp-inhibitor:	0.986
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.925
30% Bioavailability (F30%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.047
Plasma Protein Binding (PPB):	91.79808807373047%
Volume Distribution (VD):	2.458
Pgp-substrate:	2.61684513092041%

ADMET: Metabolism

CYP1A2-inhibitor:	0.037
CYP1A2-substrate:	0.633
CYP2C19-inhibitor:	0.299
CYP2C19-substrate:	0.945
CYP2C9-inhibitor:	0.372
CYP2C9-substrate:	0.109
CYP2D6-inhibitor:	0.053
CYP2D6-substrate:	0.084
CYP3A4-inhibitor:	0.889
CYP3A4-substrate:	0.791

ADMET: Excretion

Clearance (CL):	6.161
Half-life (T1/2):	0.138

ADMET: Toxicity

hERG Blockers:	0.056
Human Hepatotoxicity (H-HT):	0.767
Drug-inuced Liver Injury (DILI):	0.716
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.235
Maximum Recommended Daily Dose:	0.321
Skin Sensitization:	0.067
Carcinogencity:	0.398
Eye Corrosion:	0.148
Eye Irritation:	0.048
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC15498

Natural Product ID:	NPC15498
*Common Name:**	ACPQHJVBMJBRJO-BCTXLRGRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ACPQHJVBMJBRJO-BCTXLRGRSA-N
Standard InCHI:	InChI=1S/C32H48O4/c1-18(2)16-23-28(35-20(4)33)19(3)27-24(36-23)17-32(9)22-10-11-25-29(5,6)26(34)13-14-30(25,7)21(22)12-15-31(27,32)8/h16,19,23-25,27-28H,10-15,17H2,1-9H3/t19-,23-,24+,25+,27-,28+,30+,31+,32-/m0/s1
SMILES:	CC(=C[C@H]1[C@@H]([C@@H](C)[C@H]2[C@@H](C[C@@]3(C)C4=C(CC[C@]23C)[C@@]2(C)CCC(=O)C(C)(C)[C@H]2CC4)O1)OC(=O)C)C
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: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
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	small food enterprises (Zvijezda d.d., Zagreb, Croatia)	n.a.	DOI[10.1002/EJLT.200900231]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16660462]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	flower petals	n.a.	n.a.	PMID[17480100]
NPO12687	Planktothrix rubescens	Species	Microcoleaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17935298]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[6361218]
NPO18949	Erythrina eriotricha	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[8590641]
NPO26686	Eleutherobia aurea	Species	Parasphaerascleridae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322360]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Flower Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Pollen Or Spore	n.a.	n.a.	Database[FooDB]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO454	Helianthus annuus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18139	Potentilla anserina	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13846	Crinodendron hookerianum	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15187	Aloe marlothii	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18949	Erythrina eriotricha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12687	Planktothrix rubescens	Species	Microcoleaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26686	Eleutherobia aurea	Species	Parasphaerascleridae	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 NPC15498 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	220
0.1-0.2	1226
0.2-0.3	4646
0.3-0.4	12805
0.4-0.5	9150
0.5-0.6	6503
0.6-0.7	6355
0.7-0.8	1722
0.8-0.85	67
0.85-0.9	3
0.9-0.95	0
0.95-1	0

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 NPC15498 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	1449
0.2-0.3	3904
0.3-0.4	2451
0.4-0.5	662
0.5-0.6	183
0.6-0.7	229
0.7-0.8	78
0.8-0.85	10
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