NPASS Compound

Structure

NPC79916 OpenBabel06302216142D 24 26 0 0 1 0 0 0 0 0999 V2000 -2.9814 -2.4363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2690 -1.7345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5922 -0.7882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0538 0.0545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0593 0.1591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3575 -0.5533 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6236 -0.3600 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4689 0.1743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3543 -0.2905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3944 -1.2897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5491 -1.8241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5893 -2.8233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7440 -3.3576 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2798 -1.7546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3199 -2.7538 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1106 -1.2335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4304 -1.9665 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4769 -1.5461 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3276 -2.0718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8826 -0.9512 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6703 -0.2631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0747 0.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8714 -1.1002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 19 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 18 1 0 0 0 0 7 22 1 0 0 0 0 7 8 1 6 0 0 0 7 16 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 14 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 20 24 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	220.18
Volume:	248.481
LogP:	4.041
LogD:	3.84
LogS:	-4.054
# Rotatable Bonds:	0
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.619
Synthetic Accessibility Score:	5.538
Fsp3:	0.867
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:	-4.6
MDCK Permeability:	1.670522033236921e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.099
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.767
Plasma Protein Binding (PPB):	89.41634368896484%
Volume Distribution (VD):	1.221
Pgp-substrate:	12.381882667541504%

ADMET: Metabolism

CYP1A2-inhibitor:	0.053
CYP1A2-substrate:	0.737
CYP2C19-inhibitor:	0.209
CYP2C19-substrate:	0.935
CYP2C9-inhibitor:	0.183
CYP2C9-substrate:	0.936
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.805
CYP3A4-inhibitor:	0.041
CYP3A4-substrate:	0.213

ADMET: Excretion

Clearance (CL):	5.913
Half-life (T1/2):	0.064

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.245
Drug-inuced Liver Injury (DILI):	0.033
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.44
Maximum Recommended Daily Dose:	0.399
Skin Sensitization:	0.027
Carcinogencity:	0.097
Eye Corrosion:	0.013
Eye Irritation:	0.622
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: NPC79916

Natural Product ID:	NPC79916
*Common Name:**	JRXVBCYCCXXJHE-IXHPFPMNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JRXVBCYCCXXJHE-IXHPFPMNSA-N
Standard InCHI:	InChI=1S/C20H32O4/c1-14-4-3-5-17-19(8-6-16(12-22)7-9-21)13-24-20(17,11-14)18(23)10-15(19)2/h4,7,15,17-18,21-23H,3,5-6,8-13H2,1-2H3/b16-7-/t15-,17-,18+,19-,20-/m1/s1
SMILES:	CC1=CCC[C@@H]2[C@]3(CC/C(=C/CO)/CO)CO[C@@]2(C1)[C@H](C[C@H]3C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46902093
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols

*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
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26562741]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29517238]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31625751]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	Along the Valencian coast, Spain	2020-Jun&Jul	PMID[35161358]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Herb	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	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 NPC79916 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	173
0.1-0.2	1429
0.2-0.3	4707
0.3-0.4	12411
0.4-0.5	10823
0.5-0.6	7272
0.6-0.7	4862
0.7-0.8	972
0.8-0.85	46
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 NPC79916 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	152
0.1-0.2	1809
0.2-0.3	3996
0.3-0.4	2184
0.4-0.5	614
0.5-0.6	275
0.6-0.7	104
0.7-0.8	16
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