NPASS Compound

Structure

NPC76884 OpenBabel06302215552D 24 27 0 0 1 0 0 0 0 0999 V2000 3.3300 -0.4447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3868 -0.6452 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9946 -1.5262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0356 -1.4254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 -0.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 1.9286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 1.4464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6702 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6702 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6702 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 1.4464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8351 1.4464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8351 -0.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8351 -1.4464 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5053 -0.4821 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3404 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 2.4107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.8929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 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 19 1 0 0 0 0 5 6 1 1 0 0 0 5 11 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 9 23 1 0 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	329.16
Volume:	335.93
LogP:	1.683
LogD:	1.532
LogS:	-2.923
# Rotatable Bonds:	2
TPSA:	59.0
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.901
Synthetic Accessibility Score:	4.137
Fsp3:	0.526
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.855
MDCK Permeability:	2.2118012566352263e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.009
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.956
30% Bioavailability (F30%):	0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.998
Plasma Protein Binding (PPB):	52.43891906738281%
Volume Distribution (VD):	1.8
Pgp-substrate:	43.31806945800781%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.905
CYP2C19-inhibitor:	0.378
CYP2C19-substrate:	0.933
CYP2C9-inhibitor:	0.245
CYP2C9-substrate:	0.598
CYP2D6-inhibitor:	0.306
CYP2D6-substrate:	0.829
CYP3A4-inhibitor:	0.714
CYP3A4-substrate:	0.938

ADMET: Excretion

Clearance (CL):	9.044
Half-life (T1/2):	0.647

ADMET: Toxicity

hERG Blockers:	0.072
Human Hepatotoxicity (H-HT):	0.775
Drug-inuced Liver Injury (DILI):	0.033
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.7
Maximum Recommended Daily Dose:	0.92
Skin Sensitization:	0.06
Carcinogencity:	0.91
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC76884

Natural Product ID:	NPC76884
*Common Name:**	RARWEROUOQPTCJ-RBUKOAKNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RARWEROUOQPTCJ-RBUKOAKNSA-N
Standard InCHI:	InChI=1S/C19H23NO4/c1-20-9-8-18-10-13(21)15(24-3)11-19(18,20)7-6-12-4-5-14(23-2)17(22)16(12)18/h4-5,11,22H,6-10H2,1-3H3/t18-,19+/m0/s1
SMILES:	CN1CC[C@]23CC(=O)C(=C[C@@]13CCc1ccc(c(c21)O)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12302744
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002792] Hasubanan alkaloids

*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
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12542368]
NPO21740	Ajuga salicifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12713393]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	stem	n.a.	PMID[21214233]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21214233]
NPO22181	Leibnitzia anandria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24699147]
NPO21410	Populus balsamifera	Species	Salicaceae	Eukaryota	Buds	n.a.	n.a.	PMID[25927817]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28139925]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31184894]
NPO7002	Ardisia hortorum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21410	Populus balsamifera	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7002	Ardisia hortorum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22181	Leibnitzia anandria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21410	Populus balsamifera	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21410	Populus balsamifera	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19668.1	Euphorbia characias subsp. wulfenii	Subspecies	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20965	Oxytropis lanata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22181	Leibnitzia anandria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20581	Sargassum fulvellum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22436	Lora quadra	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO19888	Doronicum grandiflorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14677	Brachylaena neriifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20325	Dictyodendrilla cavernosa	Species	Dictyodendrillidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22942	Moesziomyces antarcticus	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21740	Ajuga salicifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22629	Spongia vaginalis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22514	Cetraria cucullata	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22390	Virola theiodora	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21468	Dilophus guineensis	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20704	Conus gladiator	Species	Conidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18333	Sphaerophysa salsula	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22498	Lithocarpus haipinii	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21780	Strychnos gossweileri	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7002	Ardisia hortorum	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20961	Hugonia oreogena	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21410	Populus balsamifera	Species	Salicaceae	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 NPC76884 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	290
0.1-0.2	1361
0.2-0.3	4076
0.3-0.4	11456
0.4-0.5	6479
0.5-0.6	11989
0.6-0.7	6491
0.7-0.8	535
0.8-0.85	13
0.85-0.9	4
0.9-0.95	2
0.95-1	1

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 NPC76884 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	196
0.1-0.2	691
0.2-0.3	1104
0.3-0.4	2195
0.4-0.5	2679
0.5-0.6	1684
0.6-0.7	513
0.7-0.8	80
0.8-0.85	7
0.85-0.9	0
0.9-0.95	1
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