NPASS Compound

Structure

NPC9713 OpenBabel06302215272D 25 30 0 0 1 0 0 0 0 0999 V2000 -1.4626 -2.0822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9748 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 -2.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4882 -3.7712 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -1.9513 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8444 -1.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8445 -0.4878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3666 0.1093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2253 0.8898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5270 1.2660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2025 0.9545 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 1.1729 1.0568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5701 0.1656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8452 -0.4876 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5349 -0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3800 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2246 -0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2248 -1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3803 -1.9508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5351 -1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6905 -1.9511 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8453 -1.4635 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0004 -1.9513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8445 -1.4635 0.0000 C 0 0 0 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 5 22 1 0 0 0 0 7 6 1 6 0 0 0 7 24 1 0 0 0 0 7 25 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 25 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 22 1 0 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 20 2 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 2 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	338.2
Volume:	349.462
LogP:	2.315
LogD:	2.326
LogS:	-4.171
# Rotatable Bonds:	2
TPSA:	41.57
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	7
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.8
Synthetic Accessibility Score:	5.897
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.834
MDCK Permeability:	3.33190182573162e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.932
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.752
30% Bioavailability (F30%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.988
Plasma Protein Binding (PPB):	48.86363983154297%
Volume Distribution (VD):	1.811
Pgp-substrate:	59.14368438720703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.121
CYP1A2-substrate:	0.819
CYP2C19-inhibitor:	0.144
CYP2C19-substrate:	0.873
CYP2C9-inhibitor:	0.247
CYP2C9-substrate:	0.161
CYP2D6-inhibitor:	0.874
CYP2D6-substrate:	0.884
CYP3A4-inhibitor:	0.915
CYP3A4-substrate:	0.717

ADMET: Excretion

Clearance (CL):	6.206
Half-life (T1/2):	0.331

ADMET: Toxicity

hERG Blockers:	0.182
Human Hepatotoxicity (H-HT):	0.216
Drug-inuced Liver Injury (DILI):	0.064
AMES Toxicity:	0.157
Rat Oral Acute Toxicity:	0.804
Maximum Recommended Daily Dose:	0.931
Skin Sensitization:	0.705
Carcinogencity:	0.211
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.761

Download Data

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

Natural Product: NPC9713

Natural Product ID:	NPC9713
*Common Name:**	IYLRRIUNGGQRTN-NWRWZVFGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IYLRRIUNGGQRTN-NWRWZVFGSA-N
Standard InCHI:	InChI=1S/C21H26N2O2/c1-25-17(24)15-13-19-7-4-11-23-12-10-20(18(19)23)14-5-2-3-6-16(14)22-21(15,20)9-8-19/h2-3,5-6,15,18,22H,4,7-13H2,1H3/t15-,18-,19+,20+,21+/m0/s1
SMILES:	COC(=O)[C@@H]1C[C@@]23CCCN4CC[C@@]5(c6ccccc6N[C@]15CC2)[C@H]34
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	7069830
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003755] Aspidofractine alkaloids

*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
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11551759]
NPO18923	Coleus xanthanthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027731]
NPO10	Alexandrium ostenfeldii	Species	Pyrocystaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872129]
NPO10	Alexandrium ostenfeldii	Species	Pyrocystaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19572609]
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21214467]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21428274]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	stem	n.a.	PMID[21428274]
NPO17129	Melodinus hemsleyanus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32683864]
NPO18923	Coleus xanthanthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18923	Coleus xanthanthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28069.1	Artemisia cana subsp. viscidula	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17129	Melodinus hemsleyanus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21640	Pygmaeopremna herbacea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13485	Prismatomeris sessiliflora	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8358	Senecio halimifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19196	Lecocarpus pinnatifidus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20028	Lethariella sernanderi	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10	Alexandrium ostenfeldii	Species	Pyrocystaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18923	Coleus xanthanthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17662	Scutellaria glabrata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3634	Robinia pseudoacacia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11492	Kopsia grandifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17129	Melodinus hemsleyanus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3679	Psilocybe baeocystis	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17897	Streptomyces albospinus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO21313	Rabdosia lasiocarpa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28069.1	Artemisia cana subsp. viscidula	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3460	Vepris uguenensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1824	Callitris rhomboidea	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2744	Aphloia madagascariensis	Species	Aphloiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21640	Pygmaeopremna herbacea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO671	Kopsia larutensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7972	Solaster endeca	Species	Solasteridae	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

Activity Type	# Activity
EC50	1

Activity Type	# Activity
TISSUE	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT26252	TISSUE	Aortic artery	Rattus norvegicus	EC50	>	10000.0	nM	PMID[32683864]

☑ 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 NPC9713 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	282
0.1-0.2	1400
0.2-0.3	5380
0.3-0.4	23127
0.4-0.5	8908
0.5-0.6	2859
0.6-0.7	549
0.7-0.8	150
0.8-0.85	27
0.85-0.9	5
0.9-0.95	4
0.95-1	6

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 NPC9713 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	537
0.2-0.3	795
0.3-0.4	1748
0.4-0.5	3761
0.5-0.6	1917
0.6-0.7	214
0.7-0.8	9
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