NPASS Compound

Structure

NPC63724 OpenBabel06302215132D 22 25 0 0 1 0 0 0 0 0999 V2000 -0.2788 -1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3690 0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2709 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 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 1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 21 1 0 0 0 0 2 3 2 0 0 0 0 3 19 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 17 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 1 0 0 0 0 9 11 1 0 0 0 0 9 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 6 0 0 0 15 17 1 0 0 0 0 17 18 1 6 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	300.21
Volume:	329.921
LogP:	5.563
LogD:	5.166
LogS:	-6.084
# Rotatable Bonds:	0
TPSA:	33.37
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.688
Synthetic Accessibility Score:	4.444
Fsp3:	0.7
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:	-4.741
MDCK Permeability:	2.122331534337718e-05
Pgp-inhibitor:	0.315
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.698

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.118
Plasma Protein Binding (PPB):	99.14923858642578%
Volume Distribution (VD):	3.131
Pgp-substrate:	2.2686736583709717%

ADMET: Metabolism

CYP1A2-inhibitor:	0.209
CYP1A2-substrate:	0.82
CYP2C19-inhibitor:	0.18
CYP2C19-substrate:	0.854
CYP2C9-inhibitor:	0.341
CYP2C9-substrate:	0.907
CYP2D6-inhibitor:	0.05
CYP2D6-substrate:	0.773
CYP3A4-inhibitor:	0.168
CYP3A4-substrate:	0.23

ADMET: Excretion

Clearance (CL):	2.769
Half-life (T1/2):	0.111

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.542
Drug-inuced Liver Injury (DILI):	0.434
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.561
Maximum Recommended Daily Dose:	0.91
Skin Sensitization:	0.832
Carcinogencity:	0.079
Eye Corrosion:	0.024
Eye Irritation:	0.543
Respiratory Toxicity:	0.966

Download Data

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

Natural Product: NPC63724

Natural Product ID:	NPC63724
*Common Name:**	ZXEVPUOHSXARBR-VIPLHTEESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZXEVPUOHSXARBR-VIPLHTEESA-N
Standard InCHI:	InChI=1S/C20H28O2/c1-12-14-10-13-6-7-17-19(2,3)8-5-9-20(17,4)15(13)11-16(14)22-18(12)21/h10,15-17H,5-9,11H2,1-4H3/t15-,16-,17-,20+/m1/s1
SMILES:	CC1=C2C=C3CC[C@@H]4C(C)(C)CCC[C@@]4(C)[C@@H]3C[C@H]2OC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5318716
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1021/np0201523]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193012]
NPO26661	Heimia salicifolia	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3783154]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21375	Euphorbia nematocypha	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26172	Dryopteris sacrosancta	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21375	Euphorbia nematocypha	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21375	Euphorbia nematocypha	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26931	Dolichothele uberiformis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21295	Botryotrichum piluliferum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26411	Stemphylium radicinum	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26661	Heimia salicifolia	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26433	Conus marmoreus	Species	Conidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26568	Rubus koehneanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21375	Euphorbia nematocypha	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25876	Chromodoris inornata	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26383	Lemna trisulca	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26888	Narcissus asturiensis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29041	Scutellaria orientalis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4283	Tripteris vaillantii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26172	Dryopteris sacrosancta	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26190	Aspergillus wentii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26215	Eleusine indica	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21065	Euphorbia calyptrata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21665.1	Mycobacterium avium subsp. paratuberculosis	Subspecies	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26906	Astragalus interpositus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26839	Microlepia speluncae	Species	Dennstaedtiaceae	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 NPC63724 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	187
0.1-0.2	1065
0.2-0.3	4244
0.3-0.4	12735
0.4-0.5	11087
0.5-0.6	7619
0.6-0.7	4598
0.7-0.8	1053
0.8-0.85	84
0.85-0.9	21
0.9-0.95	4
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 NPC63724 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	1169
0.2-0.3	3728
0.3-0.4	2721
0.4-0.5	905
0.5-0.6	256
0.6-0.7	181
0.7-0.8	20
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