NPASS Compound

Structure

NPC278625 OpenBabel06302215542D 25 29 0 0 0 0 0 0 0 0999 V2000 2.5339 1.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5337 0.4871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6892 -0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8445 0.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8447 1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6896 1.9504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8446 1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6894 1.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5338 1.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5340 0.4881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4620 0.1868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8590 -0.7044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8293 -0.8062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4026 -0.0168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0056 0.8744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0353 0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4616 1.7654 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6897 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8448 0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6899 -0.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4147 -1.6270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7627 -1.2762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5602 -2.2299 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0380 -0.6239 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 20 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 19 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 17 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 18 2 0 0 0 0 11 16 2 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 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.08
Volume:	331.057
LogP:	4.495
LogD:	3.16
LogS:	-5.292
# Rotatable Bonds:	2
TPSA:	85.95
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.335
Synthetic Accessibility Score:	2.492
Fsp3:	0.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.545
MDCK Permeability:	5.866353603778407e-06
Pgp-inhibitor:	0.005
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.623
20% Bioavailability (F20%):	0.164
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.103
Plasma Protein Binding (PPB):	95.78974914550781%
Volume Distribution (VD):	0.382
Pgp-substrate:	2.7535171508789062%

ADMET: Metabolism

CYP1A2-inhibitor:	0.985
CYP1A2-substrate:	0.162
CYP2C19-inhibitor:	0.165
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.493
CYP2C9-substrate:	0.614
CYP2D6-inhibitor:	0.791
CYP2D6-substrate:	0.325
CYP3A4-inhibitor:	0.278
CYP3A4-substrate:	0.057

ADMET: Excretion

Clearance (CL):	1.573
Half-life (T1/2):	0.364

ADMET: Toxicity

hERG Blockers:	0.021
Human Hepatotoxicity (H-HT):	0.801
Drug-inuced Liver Injury (DILI):	0.985
AMES Toxicity:	0.226
Rat Oral Acute Toxicity:	0.052
Maximum Recommended Daily Dose:	0.922
Skin Sensitization:	0.949
Carcinogencity:	0.583
Eye Corrosion:	0.009
Eye Irritation:	0.982
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC278625

Natural Product ID:	NPC278625
*Common Name:**	WHEPTQIRTYUHFN-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WHEPTQIRTYUHFN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H12N2O3/c23-19(20(24)25)17-16-11-6-2-4-8-14(11)21-15(16)9-12-10-5-1-3-7-13(10)22-18(12)17/h1-9,21-22H,(H,24,25)
SMILES:	c1ccc2c(c1)c1cc3c(c4ccccc4[nH]3)c(c1[nH]2)C(=O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10131461
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0000210] Carbazoles [CHEMONTID:0001865] Pyrrolocarbazoles [CHEMONTID:0001866] Indolocarbazoles

*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
NPO2794	Salvia clevelandii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17190465]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22029392]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26081757]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[27169184]
NPO5990	Frangula alnus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3130	Ainsliaea acerifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14184	Scoliodon walbeehmi	Species	Carcharhinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9156	Cystophora congesta	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11502	Polystichum aculeatum	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5990	Frangula alnus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10797	Nerine corusca	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23765.1	Cotoneaster salicifolius var. henryanus	Varieties	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5500	Protea eximia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2794	Salvia clevelandii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2494	Xanthium strumarium	Species	Asteraceae	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 NPC278625 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	424
0.1-0.2	2793
0.2-0.3	13129
0.3-0.4	17067
0.4-0.5	5230
0.5-0.6	2229
0.6-0.7	1528
0.7-0.8	295
0.8-0.85	2
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 NPC278625 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	292
0.1-0.2	656
0.2-0.3	886
0.3-0.4	2218
0.4-0.5	2860
0.5-0.6	1671
0.6-0.7	507
0.7-0.8	59
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