NPASS Compound

Structure

NPC198137 OpenBabel06302215372D 37 41 0 0 1 0 0 0 0 0999 V2000 1.1248 0.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6594 -1.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5622 0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5622 0.6340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5622 -1.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 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 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 33 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 32 1 0 0 0 0 6 7 1 0 0 0 0 6 34 1 1 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 14 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 32 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 19 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 31 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 1 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 32 33 1 6 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	252.08
Volume:	264.902
LogP:	4.232
LogD:	2.95
LogS:	-3.675
# Rotatable Bonds:	1
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.456
Synthetic Accessibility Score:	2.498
Fsp3:	0.0
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:	-5.064
MDCK Permeability:	1.240275742020458e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.092
20% Bioavailability (F20%):	0.967
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.011
Plasma Protein Binding (PPB):	98.1205062866211%
Volume Distribution (VD):	0.51
Pgp-substrate:	3.6385159492492676%

ADMET: Metabolism

CYP1A2-inhibitor:	0.982
CYP1A2-substrate:	0.14
CYP2C19-inhibitor:	0.075
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.569
CYP2C9-substrate:	0.619
CYP2D6-inhibitor:	0.675
CYP2D6-substrate:	0.444
CYP3A4-inhibitor:	0.131
CYP3A4-substrate:	0.103

ADMET: Excretion

Clearance (CL):	8.333
Half-life (T1/2):	0.635

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.096
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.765
Rat Oral Acute Toxicity:	0.558
Maximum Recommended Daily Dose:	0.894
Skin Sensitization:	0.949
Carcinogencity:	0.685
Eye Corrosion:	0.01
Eye Irritation:	0.948
Respiratory Toxicity:	0.835

Download Data

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

Natural Product: NPC198137

Natural Product ID:	NPC198137
*Common Name:**	DOKJMAPUMWPNMW-BZWRLGBTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DOKJMAPUMWPNMW-BZWRLGBTSA-N
Standard InCHI:	InChI=1S/C31H48O6/c1-27(2)14-15-31(26(35)37-7)13-10-19-18(20(31)16-27)8-9-22-28(19,3)12-11-23-29(22,4)17-21(32)24(33)30(23,5)25(34)36-6/h20-24,32-33H,8-17H2,1-7H3/t20-,21-,22-,23+,24-,28-,29+,30-,31+/m0/s1
SMILES:	CC1(C)CC[C@@]2(CCC3=C(CC[C@H]4[C@@]3(C)CC[C@@H]3[C@]4(C)C[C@@H]([C@@H]([C@@]3(C)C(=O)OC)O)O)[C@@H]2C1)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:0000258] Steroids and steroid derivatives [CHEMONTID:0001295] Hydroxysteroids [CHEMONTID:0003241] 12-hydroxysteroids [CHEMONTID:0003242] 12-alpha-hydroxysteroids

*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
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)94055-X]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	flower	n.a.	DOI[10.3390/70200245]
NPO27808	Cremanthodium discoideum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10579856]
NPO27081	Clavularia inflata	Species	Clavulariidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[11520220]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24617303]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28491	Astrotrichilia voamatata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20099	Petalostylis labicheoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27846	Aeodes ulvoidea	Species	Halymeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28081	Actinoplanes arizonaensis	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28491	Astrotrichilia voamatata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28476	Doris tricolor	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19588	Piper coruscans	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28312	Lentinus squarrosulus	Species	Lentinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28028	Aquilegia atrata	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28154	Acrodontium salmoneum	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3513	Fuscoporia senex	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29361	Chondrus yendoi	Species	Gigartinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17149	Heracleum candicans	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28261	Pyrophorus pellucens	Species	Elateridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8672	Ophiura ophiura	Species	Ophiuridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27622	Ligularia cyathiceps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27808	Cremanthodium discoideum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28102	Baccharis tucumanensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28210	Myrmecia gulosa	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28521	Delphinium vestitum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27081	Clavularia inflata	Species	Clavulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27934	Mezilaurus synandra	Species	Lauraceae	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 NPC198137 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	248
0.1-0.2	1685
0.2-0.3	5159
0.3-0.4	12589
0.4-0.5	10105
0.5-0.6	5576
0.6-0.7	4949
0.7-0.8	2075
0.8-0.85	217
0.85-0.9	86
0.9-0.95	8
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 NPC198137 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	227
0.1-0.2	2103
0.2-0.3	3771
0.3-0.4	1977
0.4-0.5	637
0.5-0.6	215
0.6-0.7	194
0.7-0.8	23
0.8-0.85	3
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