NPASS Compound

Structure

NPC472192 OpenBabel07101718332D 23 26 0 0 1 0 0 0 0 0999 V2000 3.5085 -2.4862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6180 1.9021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3601 1.6942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 -0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 -2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 -1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2872 1.1590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4563 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0962 -2.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 -1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4781 -0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1180 -2.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 -1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 -0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7653 -1.8171 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9781 0.2079 0.0000 N 0 3 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 -3.5686 -2.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4489 -3.0955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7164 -1.5081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 2 8 1 0 0 0 0 3 9 1 0 0 0 0 4 6 2 0 0 0 0 4 12 1 0 0 0 0 5 7 2 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 7 13 1 0 0 0 0 8 19 1 0 0 0 0 9 20 1 0 0 0 0 10 14 1 0 0 0 0 10 18 1 0 0 0 0 11 15 1 0 0 0 0 11 18 1 0 0 0 0 12 17 2 3 0 0 0 13 21 2 0 0 0 0 14 16 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 15 22 2 0 0 0 0 16 17 1 0 0 0 0 17 20 1 0 0 0 0 18 1 1 1 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 M CHG 1 19 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	295.14
Volume:	308.095
LogP:	3.593
LogD:	3.297
LogS:	-3.469
# Rotatable Bonds:	1
TPSA:	49.27
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.678
Synthetic Accessibility Score:	3.047
Fsp3:	0.278
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.943
MDCK Permeability:	1.8476295736036263e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.099
20% Bioavailability (F20%):	0.99
30% Bioavailability (F30%):	0.709

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.828
Plasma Protein Binding (PPB):	92.74047088623047%
Volume Distribution (VD):	0.943
Pgp-substrate:	6.501317977905273%

ADMET: Metabolism

CYP1A2-inhibitor:	0.867
CYP1A2-substrate:	0.918
CYP2C19-inhibitor:	0.082
CYP2C19-substrate:	0.071
CYP2C9-inhibitor:	0.067
CYP2C9-substrate:	0.709
CYP2D6-inhibitor:	0.862
CYP2D6-substrate:	0.907
CYP3A4-inhibitor:	0.116
CYP3A4-substrate:	0.155

ADMET: Excretion

Clearance (CL):	9.655
Half-life (T1/2):	0.641

ADMET: Toxicity

hERG Blockers:	0.086
Human Hepatotoxicity (H-HT):	0.053
Drug-inuced Liver Injury (DILI):	0.362
AMES Toxicity:	0.849
Rat Oral Acute Toxicity:	0.068
Maximum Recommended Daily Dose:	0.85
Skin Sensitization:	0.82
Carcinogencity:	0.797
Eye Corrosion:	0.009
Eye Irritation:	0.87
Respiratory Toxicity:	0.72

Download Data

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

Natural Product: NPC472192

Natural Product ID:	NPC472192
*Common Name:**	OVLDHOAUOKJCIX-SFHVURJKSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OVLDHOAUOKJCIX-SFHVURJKSA-O
Standard InCHI:	InChI=1S/C18H20N2O3/c1-18(23)10-14-16(15(22)11-18)17(12-4-6-13(21)7-5-12)20-9-3-2-8-19(14)20/h4-7,23H,2-3,8-11H2,1H3/p+1/t18-/m0/s1
SMILES:	O=C1C=CC(=c2n3CCCC[n+]3c3c2C(=O)C[C@@](C3)(C)O)C=C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3344046
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001629] Benzopyrazoles [CHEMONTID:0000080] Indazoles [CHEMONTID:0001856] Pyridazinoindazoles

*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
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	seeds	n.a.	n.a.	PMID[25299458]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO12297	Nigella sativa	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12297	Nigella sativa	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	Activity	=	8.0	%	PMID[501035]

☑ 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 NPC472192 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Natural Product ID
0.6796	Remote Similarity	NPC472194
0.6218	Remote Similarity	NPC34193
0.6083	Remote Similarity	NPC314792
0.6048	Remote Similarity	NPC24596
0.5935	Remote Similarity	NPC9436
0.5918	Remote Similarity	NPC201899
0.5918	Remote Similarity	NPC471674
0.5882	Remote Similarity	NPC475610
0.5878	Remote Similarity	NPC471673
0.5862	Remote Similarity	NPC236322
0.5827	Remote Similarity	NPC72688
0.5806	Remote Similarity	NPC87919
0.5806	Remote Similarity	NPC133420
0.5789	Remote Similarity	NPC476141
0.5772	Remote Similarity	NPC251884
0.576	Remote Similarity	NPC185929
0.5748	Remote Similarity	NPC175585
0.5714	Remote Similarity	NPC176773
0.5652	Remote Similarity	NPC96010
0.5652	Remote Similarity	NPC317654
0.5649	Remote Similarity	NPC176336

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 NPC472192 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5746	Remote Similarity	NPD7739	Clinical (unspecified phase)
0.5704	Remote Similarity	NPD7623	Phase 3
0.5704	Remote Similarity	NPD7624	Clinical (unspecified phase)

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