NPASS Compound

Structure

NPC293832 OpenBabel06302215502D 29 34 0 0 1 0 0 0 0 0999 V2000 1.5068 -0.8699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5023 -0.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0045 -1.7399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5068 -0.8699 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0760 -1.6533 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7655 -2.6087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9969 -1.3541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9969 -0.3858 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8356 0.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6753 -1.3534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5151 -1.8376 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3542 -1.3525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1940 -1.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1946 -2.8060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0341 -3.2897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0344 -4.2586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1952 -4.7437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3557 -4.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3554 -3.2912 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4897 -3.7917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5157 -2.8070 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6770 -3.2919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8372 -2.8077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8367 -1.8383 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9709 -2.3388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0760 -0.0865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0045 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 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 29 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 27 1 0 0 0 0 5 6 1 0 0 0 0 5 28 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 25 1 0 0 0 0 9 10 1 0 0 0 0 9 27 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 20 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 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 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	396.3
Volume:	436.517
LogP:	6.498
LogD:	4.919
LogS:	-6.278
# Rotatable Bonds:	0
TPSA:	18.46
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.464
Synthetic Accessibility Score:	5.377
Fsp3:	0.852
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:	-4.953
MDCK Permeability:	2.4831248083501123e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.979
30% Bioavailability (F30%):	0.491

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.085
Plasma Protein Binding (PPB):	97.30980682373047%
Volume Distribution (VD):	1.948
Pgp-substrate:	1.8328627347946167%

ADMET: Metabolism

CYP1A2-inhibitor:	0.091
CYP1A2-substrate:	0.527
CYP2C19-inhibitor:	0.368
CYP2C19-substrate:	0.929
CYP2C9-inhibitor:	0.376
CYP2C9-substrate:	0.078
CYP2D6-inhibitor:	0.359
CYP2D6-substrate:	0.857
CYP3A4-inhibitor:	0.891
CYP3A4-substrate:	0.651

ADMET: Excretion

Clearance (CL):	8.884
Half-life (T1/2):	0.156

ADMET: Toxicity

hERG Blockers:	0.994
Human Hepatotoxicity (H-HT):	0.452
Drug-inuced Liver Injury (DILI):	0.403
AMES Toxicity:	0.028
Rat Oral Acute Toxicity:	0.204
Maximum Recommended Daily Dose:	0.739
Skin Sensitization:	0.99
Carcinogencity:	0.431
Eye Corrosion:	0.698
Eye Irritation:	0.484
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC293832

Natural Product ID:	NPC293832
*Common Name:**	YEQBGJNMHDZXRG-VGIWDKIDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YEQBGJNMHDZXRG-VGIWDKIDSA-N
Standard InCHI:	InChI=1S/C27H40O2/c1-17-10-14-27(28-16-17)18(2)24-23(29-27)15-22-20-9-8-19-7-5-6-12-25(19,3)21(20)11-13-26(22,24)4/h5,7-8,17-18,20-24H,6,9-16H2,1-4H3/t17-,18+,20-,21-,22+,23+,24+,25+,26+,27-/m1/s1
SMILES:	C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C=CCC[C@]6(C)[C@@H]5CC[C@]34C)O2)OC1
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
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11473431]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575945]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11599360]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18163582]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381697]
NPO26918	Taricha granulosa	Species	Salamandridae	Eukaryota	n.a.	n.a.	n.a.	PMID[32896120]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO433	Geranium sibiricum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO433	Geranium sibiricum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1463	Corethrodendron scoparium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17338	Solanum asperum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22402	Lupinus mutabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19482	Tapinoma nigerrimum	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20402	Ageratina gilbertii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20244	Melicope semecarpifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4582	Baphicacanthus cusia	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14627	Caloscypha fulgens	Species	Caloscyphaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22836	Alpinia mutica	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26918	Taricha granulosa	Species	Salamandridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23001	Halimium umbellatum	Species	Cistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23067	Shorea maranti	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4593	Lagerstroemia indica	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14100	Persea kusanoi	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7639	Senecio isatideus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO433	Geranium sibiricum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20565	Aplysina fulva	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14902	Pteris marginata	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22018	Hydrangea chinensis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18364	Genista lusitanica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2263	Croton megistocarpus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8075	Cacospongia scalaris	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12967	Reseda suffruticosa	Species	Resedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16398	Nicotiana alata	Species	Solanaceae	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 NPC293832 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	279
0.1-0.2	1465
0.2-0.3	7340
0.3-0.4	15670
0.4-0.5	7841
0.5-0.6	6796
0.6-0.7	2934
0.7-0.8	363
0.8-0.85	7
0.85-0.9	2
0.9-0.95	0
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 NPC293832 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	217
0.1-0.2	1548
0.2-0.3	4649
0.3-0.4	2005
0.4-0.5	346
0.5-0.6	195
0.6-0.7	172
0.7-0.8	18
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