NPASS Compound

Structure

NPC43885 OpenBabel06302215242D 27 26 0 0 0 0 0 0 0 0999 V2000 10.3923 -17.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -15.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -14.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -12.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 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 0 0 0 0 16 17 1 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 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	382.38
Volume:	455.9
LogP:	10.468
LogD:	4.657
LogS:	-7.346
# Rotatable Bonds:	23
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.138
Synthetic Accessibility Score:	1.76
Fsp3:	0.96
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.103
MDCK Permeability:	6.7034993662673514e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.88
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.033
Plasma Protein Binding (PPB):	97.06302642822266%
Volume Distribution (VD):	3.814
Pgp-substrate:	1.095435380935669%

ADMET: Metabolism

CYP1A2-inhibitor:	0.08
CYP1A2-substrate:	0.161
CYP2C19-inhibitor:	0.18
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.057
CYP2C9-substrate:	0.966
CYP2D6-inhibitor:	0.211
CYP2D6-substrate:	0.024
CYP3A4-inhibitor:	0.229
CYP3A4-substrate:	0.025

ADMET: Excretion

Clearance (CL):	4.59
Half-life (T1/2):	0.067

ADMET: Toxicity

hERG Blockers:	0.526
Human Hepatotoxicity (H-HT):	0.019
Drug-inuced Liver Injury (DILI):	0.505
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.972
Carcinogencity:	0.03
Eye Corrosion:	0.945
Eye Irritation:	0.911
Respiratory Toxicity:	0.81

Download Data

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

Natural Product: NPC43885

Natural Product ID:	NPC43885
*Common Name:**	XUDJZDNUVZHSKZ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XUDJZDNUVZHSKZ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H50O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25(26)27-2/h3-24H2,1-2H3
SMILES:	CCCCCCCCCCCCCCCCCCCCCCCC(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	75546
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000324] Fatty acid esters [CHEMONTID:0003417] Fatty acid methyl esters

*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
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1002/elan.200403102]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2012.02.124]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[11077184]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	seed	n.a.	PMID[11540412]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[17328234]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17548953]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[18321056]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower	n.a.	PMID[21804227]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	flower buds	Henan province, China	2005-MAY	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	flower bud	n.a.	PMID[21942812]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23265495]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[24279769]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	PMID[24675423]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Bako, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Enemore, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Gedo, Ethiopia		PMID[24926420]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	Holleta, Ethiopia		PMID[24926420]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27018	Cynomorium songaricum	Species	Cynomoriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27018	Cynomorium songaricum	Species	Cynomoriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27018	Cynomorium songaricum	Species	Cynomoriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31286	Dolichos lablab	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27018	Cynomorium songaricum	Species	Cynomoriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12006	Apis mellifera	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1515	Lonicera japonica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24778	Sesamum orientale	Species	Pedaliaceae	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
NPO12006	NPC43885	n.a.	n.a.	0.045	n.a.	n.a.	%	PMID[24926420]
NPO12006	NPC43885	n.a.	n.a.	0.199	n.a.	n.a.	%	PMID[24926420]
NPO12006	NPC43885	n.a.	n.a.	0.065	n.a.	n.a.	%	PMID[24926420]
NPO12006	NPC43885	n.a.	n.a.	0.16	n.a.	n.a.	%	PMID[24926420]

☑ 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 NPC43885 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	960
0.1-0.2	15031
0.2-0.3	15598
0.3-0.4	8542
0.4-0.5	2011
0.5-0.6	310
0.6-0.7	121
0.7-0.8	67
0.8-0.85	23
0.85-0.9	16
0.9-0.95	11
0.95-1	7

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 NPC43885 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1484
0.1-0.2	5163
0.2-0.3	1714
0.3-0.4	561
0.4-0.5	156
0.5-0.6	42
0.6-0.7	18
0.7-0.8	7
0.8-0.85	2
0.85-0.9	3
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