NPASS Compound

Structure

NPC238870 OpenBabel06302215362D 27 30 0 0 1 0 0 0 0 0999 V2000 1.0317 -4.3173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7988 -3.7423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6802 -4.1191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6843 -2.7906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4513 -2.2156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3328 -2.5923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3369 -1.2638 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4554 -0.8870 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6848 -1.5603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3220 -1.3776 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1977 -1.7675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8069 -0.4765 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6230 -0.0159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6322 0.9209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8253 1.3974 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0362 2.3554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4047 0.4644 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5817 0.7366 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4095 0.1352 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2373 0.7366 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1490 0.4404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9211 1.7098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4846 2.4853 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8979 1.7098 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0092 0.9369 0.0000 O 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 -0.4222 -2.3309 0.0000 O 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 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 19 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 27 1 0 0 0 0 12 17 1 0 0 0 0 12 26 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 25 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	380.18
Volume:	373.873
LogP:	2.144
LogD:	1.645
LogS:	-4.137
# Rotatable Bonds:	4
TPSA:	91.29
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.454
Synthetic Accessibility Score:	5.879
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.984
MDCK Permeability:	5.469894313137047e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.016
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.906
Plasma Protein Binding (PPB):	44.42979431152344%
Volume Distribution (VD):	1.085
Pgp-substrate:	48.22574996948242%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.231
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.779
CYP2C9-inhibitor:	0.023
CYP2C9-substrate:	0.035
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.494
CYP3A4-substrate:	0.436

ADMET: Excretion

Clearance (CL):	8.845
Half-life (T1/2):	0.379

ADMET: Toxicity

hERG Blockers:	0.301
Human Hepatotoxicity (H-HT):	0.74
Drug-inuced Liver Injury (DILI):	0.453
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.941
Maximum Recommended Daily Dose:	0.149
Skin Sensitization:	0.391
Carcinogencity:	0.49
Eye Corrosion:	0.017
Eye Irritation:	0.021
Respiratory Toxicity:	0.978

Download Data

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

Natural Product: NPC238870

Natural Product ID:	NPC238870
*Common Name:**	DMCKVYCFRJNFGZ-MLBSSZIMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DMCKVYCFRJNFGZ-MLBSSZIMSA-N
Standard InCHI:	InChI=1S/C20H28O7/c1-10(2)8-13(21)24-12-9-19(5,23)20-7-6-18(4,26-27-20)16(20)15-14(12)11(3)17(22)25-15/h6-7,10-12,14-16,23H,8-9H2,1-5H3/t11-,12-,14+,15-,16-,18+,19+,20-/m0/s1
SMILES:	CC(C)CC(=O)O[C@H]1C[C@](C)([C@]23C=C[C@](C)([C@@H]2[C@@H]2[C@@H]1[C@H](C)C(=O)O2)OO3)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:0001543] Sesquiterpene lactones [CHEMONTID:0001770] Guaianolides and derivatives

*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
NPO14864	Clerodendrum cyrtophyllum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473423]
NPO10210	Artabotrys uncinatus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575948]
NPO12347	Pseudomonas syringae	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14714872]
NPO15548	Sinularia leptoclados	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724859]
NPO10210	Artabotrys uncinatus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15166	Cephalotaxus hainanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12993	Polypodium vulgare	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12993	Polypodium vulgare	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15166	Cephalotaxus hainanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7042	Myrica arborea	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8392	Iryanthera polyneura	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10210	Artabotrys uncinatus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12993	Polypodium vulgare	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15166	Cephalotaxus hainanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3974	Ferula gummosa	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14989	Acanthothamnus aphyllus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13320	Glycosmis puberula	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11505	Nigella aristata	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9338	Polygala aureocauda	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14191	Berkheya rhapontica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15066	Iridaea membranacea	Species	Gigartinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15548	Sinularia leptoclados	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1027	Scrophularia leucoclada	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4699	Dracaena ombet	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12347	Pseudomonas syringae	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8392	Iryanthera polyneura	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11151	Arnebia decumbens	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19872	Achillea magnifica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10210	Artabotrys uncinatus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4503	Bryonopsis laciniosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14864	Clerodendrum cyrtophyllum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20070	Crinum stuhlmannii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11683	Crotalaria mitchellii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12539	Lissoclinum japonicum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22084	Stypandra imbricata	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5469	Pseudoxandra sclerocarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7042	Myrica arborea	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4518.1	Saccharothrix mutabilis subsp. capreolus	Subspecies	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12993	Polypodium vulgare	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6367	Cortinarius viola	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15166	Cephalotaxus hainanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13549	Otanthus maritimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26712	Cladrastis kentukea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12121	Streptomyces naraensis	Species	Streptomycetaceae	Bacteria	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 NPC238870 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	214
0.1-0.2	1294
0.2-0.3	5601
0.3-0.4	15110
0.4-0.5	9703
0.5-0.6	7867
0.6-0.7	2434
0.7-0.8	449
0.8-0.85	22
0.85-0.9	1
0.9-0.95	2
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 NPC238870 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	2095
0.2-0.3	3871
0.3-0.4	2121
0.4-0.5	556
0.5-0.6	257
0.6-0.7	36
0.7-0.8	8
0.8-0.85	1
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