NPASS Compound

Structure

NPC172142 OpenBabel06302216162D 25 30 0 0 1 0 0 0 0 0999 V2000 -0.2713 2.4936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2713 1.4088 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0848 0.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0848 -0.0004 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -1.0849 1.0845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1453 0.5421 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5945 0.0927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5944 -0.5427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1451 -0.9919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3413 -1.5962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1728 -1.9697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6868 -1.5961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4903 -0.9918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9396 -0.5425 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7879 -1.2185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8454 -0.9768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3157 0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4005 0.0011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8447 0.9779 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7871 1.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9392 0.5423 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4818 1.4816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5422 2.0241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5423 0.9392 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 24 1 0 0 0 0 3 4 1 0 0 0 0 4 25 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 21 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 13 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 25 1 0 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 21 20 1 1 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 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	341.24
Volume:	361.034
LogP:	4.01
LogD:	3.757
LogS:	-4.873
# Rotatable Bonds:	0
TPSA:	29.54
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.496
Synthetic Accessibility Score:	6.111
Fsp3:	0.864
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:	-4.753
MDCK Permeability:	1.3063435289950576e-05
Pgp-inhibitor:	0.054
Pgp-substrate:	0.112
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.626
30% Bioavailability (F30%):	0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.508
Plasma Protein Binding (PPB):	94.33641052246094%
Volume Distribution (VD):	1.08
Pgp-substrate:	3.0012311935424805%

ADMET: Metabolism

CYP1A2-inhibitor:	0.212
CYP1A2-substrate:	0.258
CYP2C19-inhibitor:	0.319
CYP2C19-substrate:	0.879
CYP2C9-inhibitor:	0.352
CYP2C9-substrate:	0.152
CYP2D6-inhibitor:	0.944
CYP2D6-substrate:	0.878
CYP3A4-inhibitor:	0.916
CYP3A4-substrate:	0.696

ADMET: Excretion

Clearance (CL):	9.265
Half-life (T1/2):	0.45

ADMET: Toxicity

hERG Blockers:	0.271
Human Hepatotoxicity (H-HT):	0.366
Drug-inuced Liver Injury (DILI):	0.757
AMES Toxicity:	0.306
Rat Oral Acute Toxicity:	0.131
Maximum Recommended Daily Dose:	0.876
Skin Sensitization:	0.938
Carcinogencity:	0.559
Eye Corrosion:	0.076
Eye Irritation:	0.608
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC172142

Natural Product ID:	NPC172142
*Common Name:**	AEJYSVZYGHPRNK-YTKBBHSFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AEJYSVZYGHPRNK-YTKBBHSFSA-N
Standard InCHI:	InChI=1S/C22H31NO2/c1-14-11-23-12-16-6-5-15-3-2-4-18(15)22-10-8-19(24)25-13-21(16,22)9-7-17(14)20(22)23/h4,14-17,20H,2-3,5-13H2,1H3/t14-,15-,16-,17-,20+,21-,22+/m1/s1
SMILES:	C[C@@H]1CN2C[C@H]3CC[C@H]4CCC=C4[C@@]45CCC(=O)OC[C@]35CC[C@H]1[C@H]24
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101727336
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000251] Indolizidines

*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
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170679]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	root	n.a.	PMID[20100622]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9341	Chaetomium abuense	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10259	Aralia cordata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7405	Candelaria medians	Species	Candelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2005	Rungia repens	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3332	Rhaponticum integrifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14943	Aphanamixis rohituka	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8017	Tonduzia pittieri	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9584	Delphinium zalil	Species	Ranunculaceae	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 NPC172142 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	122
0.1-0.2	925
0.2-0.3	12149
0.3-0.4	14496
0.4-0.5	10926
0.5-0.6	3905
0.6-0.7	149
0.7-0.8	25
0.8-0.85	0
0.85-0.9	0
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 NPC172142 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	109
0.1-0.2	607
0.2-0.3	3421
0.3-0.4	3727
0.4-0.5	960
0.5-0.6	301
0.6-0.7	24
0.7-0.8	1
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