NPASS Compound

Structure

NPC224878 OpenBabel06302215292D 27 29 0 0 1 0 0 0 0 0999 V2000 -3.1393 0.9062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1393 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9242 -0.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3545 -0.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5697 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7848 -0.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7848 -1.3594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5697 -1.8125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3545 -1.3594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1393 -1.8125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5697 -2.7188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.8125 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.7188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7848 -3.1719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5697 -2.7188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5697 -1.8125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4759 -1.8125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0228 -1.0277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7848 -1.3594 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7848 -0.4531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5697 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 0.9062 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1393 -3.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9242 -3.1719 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1393 -4.5313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9242 -4.9844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 22 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 12 1 0 0 0 0 8 9 1 0 0 0 0 8 11 1 0 0 0 0 9 10 1 0 0 0 0 12 19 1 0 0 0 0 12 13 1 0 0 0 0 12 24 1 1 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 16 19 1 0 0 0 0 19 20 1 1 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 6 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	376.19
Volume:	385.662
LogP:	2.959
LogD:	1.173
LogS:	-2.988
# Rotatable Bonds:	3
TPSA:	104.06
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.541
Synthetic Accessibility Score:	4.296
Fsp3:	0.619
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.659
MDCK Permeability:	1.7422531527699903e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.286
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.56
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.687
Plasma Protein Binding (PPB):	94.96739959716797%
Volume Distribution (VD):	1.737
Pgp-substrate:	4.897611141204834%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.798
CYP2C19-inhibitor:	0.07
CYP2C19-substrate:	0.863
CYP2C9-inhibitor:	0.294
CYP2C9-substrate:	0.88
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.296
CYP3A4-inhibitor:	0.105
CYP3A4-substrate:	0.446

ADMET: Excretion

Clearance (CL):	3.004
Half-life (T1/2):	0.413

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.269
Drug-inuced Liver Injury (DILI):	0.618
AMES Toxicity:	0.099
Rat Oral Acute Toxicity:	0.369
Maximum Recommended Daily Dose:	0.553
Skin Sensitization:	0.743
Carcinogencity:	0.025
Eye Corrosion:	0.003
Eye Irritation:	0.594
Respiratory Toxicity:	0.39

Download Data

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

Natural Product: NPC224878

Natural Product ID:	NPC224878
*Common Name:**	DEWFEGAYVMERFF-XERREHJYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DEWFEGAYVMERFF-XERREHJYSA-N
Standard InCHI:	InChI=1S/C21H28O6/c1-10(2)11-9-12-13(16(24)14(11)22)21(19(26)27-5)8-6-7-20(3,4)18(21)17(25)15(12)23/h9-10,15,18,22-24H,6-8H2,1-5H3/t15-,18-,21-/m0/s1
SMILES:	CC(C)c1cc2c(c(c1O)O)[C@]1(CCCC(C)(C)[C@@H]1C(=O)[C@H]2O)C(=O)OC
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:0001551] Diterpenoids

*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
NPO17119	Dalea versicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043439]
NPO18606	Achyrocline bogotensis	Species	Asteraceae	Eukaryota	n.a.	Colombian	n.a.	PMID[15844937]
NPO3291	Cynanchum auriculatum	Species	Apocynaceae	Eukaryota	n.a.	root	n.a.	PMID[18401845]
NPO17362	Alstonia yunnanensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19775092]
NPO18055	Isodon adenolomus	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21534539]
NPO18055	Isodon adenolomus	Species	Lamiaceae	Eukaryota	aerial parts	Shangrila, Yunnan Province, China	2008-AUG	PMID[21534539]
NPO12148.2	Acer pictum subsp. okamotoanum	Subspecies	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461665]
NPO18435	Tylophora atrofolliculata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17362	Alstonia yunnanensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3291	Cynanchum auriculatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18356	Stachys tuberifera	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18356	Stachys tuberifera	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3291	Cynanchum auriculatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17362	Alstonia yunnanensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18435	Tylophora atrofolliculata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17362	Alstonia yunnanensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3291	Cynanchum auriculatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4230	Protoparmeliopsis peltata	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17119	Dalea versicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19522	Arthropsis truncata	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13832	Aspilia hispida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19311	Dasymaschalon blumei	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17783	Sideritis cystosiphon	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17362	Alstonia yunnanensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10852	Felimare midatlantica	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16997	Talaromyces aculeatus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18055	Isodon adenolomus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17643	Penicillium pedemontanum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3291	Cynanchum auriculatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16990	Verbesina virgata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18356	Stachys tuberifera	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17911	Blepharisma japonicum	Species	Blepharismidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16567	Doriopsilla areolata	Species	Dendrodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15497	Caria ino	Species	Riodinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2377	Cetraria ciliaris	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18435	Tylophora atrofolliculata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13414	Senecio fuertesii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18606	Achyrocline bogotensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19580	Chamaemelum fuscatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19777	Pholiota adiposa	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4984	Salvia cana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12148.2	Acer pictum subsp. okamotoanum	Subspecies	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19638	Scutellaria albida	Species	Lamiaceae	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 NPC224878 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	312
0.1-0.2	1228
0.2-0.3	2800
0.3-0.4	5929
0.4-0.5	10620
0.5-0.6	7735
0.6-0.7	10433
0.7-0.8	3514
0.8-0.85	93
0.85-0.9	22
0.9-0.95	11
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 NPC224878 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	266
0.1-0.2	827
0.2-0.3	1658
0.3-0.4	2747
0.4-0.5	2032
0.5-0.6	1101
0.6-0.7	474
0.7-0.8	45
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