NPASS Compound

Structure

NPC8220 OpenBabel06302216172D 31 35 0 0 1 0 0 0 0 0999 V2000 -1.0936 -0.4530 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 -1.6133 1.0780 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 1 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 0 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 2 0 0 0 0 0 0 0 0 0 4.2098 -1.4583 0.0000 C 0 0 2 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 2 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 1 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 2 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 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 1 2 1 0 0 0 0 2 31 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 30 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 27 1 0 0 0 0 10 11 1 1 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 15 27 1 0 0 0 0 16 24 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 6 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 6 0 0 0 30 31 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.39
Volume:	490.807
LogP:	7.682
LogD:	5.451
LogS:	-7.26
# 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:	0.387
Synthetic Accessibility Score:	4.56
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:	-4.939
MDCK Permeability:	8.258308298536576e-06
Pgp-inhibitor:	0.68
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.969
30% Bioavailability (F30%):	0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.155
Plasma Protein Binding (PPB):	97.96759033203125%
Volume Distribution (VD):	1.314
Pgp-substrate:	1.879372239112854%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.27
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.953
CYP2C9-inhibitor:	0.168
CYP2C9-substrate:	0.249
CYP2D6-inhibitor:	0.173
CYP2D6-substrate:	0.465
CYP3A4-inhibitor:	0.498
CYP3A4-substrate:	0.677

ADMET: Excretion

Clearance (CL):	7.206
Half-life (T1/2):	0.018

ADMET: Toxicity

hERG Blockers:	0.13
Human Hepatotoxicity (H-HT):	0.296
Drug-inuced Liver Injury (DILI):	0.011
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.42
Maximum Recommended Daily Dose:	0.922
Skin Sensitization:	0.295
Carcinogencity:	0.083
Eye Corrosion:	0.289
Eye Irritation:	0.29
Respiratory Toxicity:	0.938

Download Data

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

Natural Product: NPC8220

Natural Product ID:	NPC8220
*Common Name:**	JFSHUTJDVKUMTJ-PRMJEPTFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JFSHUTJDVKUMTJ-PRMJEPTFSA-N
Standard InCHI:	InChI=1S/C30H50O/c1-25(2)15-16-27(5)17-18-29(7)20(21(27)19-25)9-10-23-28(6)13-12-24(31)26(3,4)22(28)11-14-30(23,29)8/h9,21-24,31H,10-19H2,1-8H3/t21-,22-,23-,24-,27-,28-,29+,30+/m1/s1
SMILES:	CC1(C)CC[C@]2(C)CC[C@@]3(C)C(=CC[C@@H]4[C@]5(C)CC[C@H](C(C)(C)[C@H]5CC[C@]34C)O)[C@H]2C1
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
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[12762799]
NPO19126	Lycopodium sieboldii	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14535761]
NPO17553	Pleione bulbocodioides	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23627123]
NPO20442	Croton stellatopilosus	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24286075]
NPO10023	Francoeuria undulata	Species	Asteraceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[28032767]
NPO16284	Scutellaria galericulata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21204	Achillea holosericea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16284	Scutellaria galericulata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17553	Pleione bulbocodioides	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17553	Pleione bulbocodioides	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3127	Aralia continentalis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3265	Echinops kebericho	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3127	Aralia continentalis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20628	Magnolia kachirachirai	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10023	Francoeuria undulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO597	Coprosma australis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19875	Ceratocystis ips	Species	Ceratocystidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20442	Croton stellatopilosus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20185	Lachnanthes tinctoria	Species	Haemodoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8004	Hexaplex trunculus	Species	Muricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17553	Pleione bulbocodioides	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4239	Betula neoalaskana	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21204	Achillea holosericea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6152	Ctenodiscus crispatus	Species	Ctenodiscidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8214	Stylotrichium rotundifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19665	Salvia aerea	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18555	Vernonia chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20071	Dracaena cinnabari	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2190	Persicaria filiformis	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21018	Macrozamia riedlei	Species	Zamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19126	Lycopodium sieboldii	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21330	Ilex integra	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10541	Dioscorea spongiosa	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16284	Scutellaria galericulata	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 NPC8220 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	212
0.1-0.2	1933
0.2-0.3	8365
0.3-0.4	16371
0.4-0.5	6344
0.5-0.6	4788
0.6-0.7	3337
0.7-0.8	969
0.8-0.85	237
0.85-0.9	101
0.9-0.95	13
0.95-1	27

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 NPC8220 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	224
0.1-0.2	2164
0.2-0.3	4232
0.3-0.4	1825
0.4-0.5	356
0.5-0.6	192
0.6-0.7	141
0.7-0.8	13
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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