NPASS Compound

Structure

NPC92193 OpenBabel06302216042D 30 33 0 0 0 0 0 0 0 0999 V2000 -0.4612 -1.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 -0.7431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.5827 -0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4487 -0.8364 0.0000 O 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 -2.2213 1.3272 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.1723 1.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4814 0.0672 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.4814 0.0672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0692 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0637 -0.6373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6515 -1.4463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6460 -1.3418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0527 -0.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4649 0.3808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4704 0.2762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0472 -0.3237 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7904 1.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9814 1.6060 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.9814 2.6060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8474 3.1060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7134 2.6060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5794 3.1060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5794 4.1060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7134 4.6060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8474 4.1060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4455 4.6060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 0.8660 0.0000 N 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 0.9945 -0.1045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 29 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 2 3 0 0 0 5 28 1 0 0 0 0 6 7 1 0 0 0 0 7 19 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 18 2 0 0 0 0 10 11 1 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 14 17 1 0 0 0 0 15 16 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 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	405.14
Volume:	398.69
LogP:	2.221
LogD:	2.744
LogS:	-3.199
# Rotatable Bonds:	5
TPSA:	123.28
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.612
Synthetic Accessibility Score:	3.251
Fsp3:	0.143
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.286
MDCK Permeability:	5.892821263842052e-06
Pgp-inhibitor:	0.007
Pgp-substrate:	0.615
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.099
Plasma Protein Binding (PPB):	93.06135559082031%
Volume Distribution (VD):	0.402
Pgp-substrate:	7.170974254608154%

ADMET: Metabolism

CYP1A2-inhibitor:	0.248
CYP1A2-substrate:	0.766
CYP2C19-inhibitor:	0.789
CYP2C19-substrate:	0.07
CYP2C9-inhibitor:	0.885
CYP2C9-substrate:	0.871
CYP2D6-inhibitor:	0.803
CYP2D6-substrate:	0.61
CYP3A4-inhibitor:	0.688
CYP3A4-substrate:	0.815

ADMET: Excretion

Clearance (CL):	10.425
Half-life (T1/2):	0.856

ADMET: Toxicity

hERG Blockers:	0.112
Human Hepatotoxicity (H-HT):	0.974
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.492
Rat Oral Acute Toxicity:	0.573
Maximum Recommended Daily Dose:	0.135
Skin Sensitization:	0.183
Carcinogencity:	0.879
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.054

Download Data

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

Natural Product: NPC92193

Natural Product ID:	NPC92193
*Common Name:**	MQJROUNNFORFQI-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MQJROUNNFORFQI-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H19N5O4/c1-25-19(29)18(24-21(25)30)23-20-22-15(10-13-2-6-16(27)7-3-13)12-26(20)11-14-4-8-17(28)9-5-14/h2-9,12,27-28H,10-11H2,1H3,(H,22,23,24,30)
SMILES:	CN1C(=O)C(=Nc2nc(Cc3ccc(cc3)O)cn2Cc2ccc(cc2)O)N=C1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10363904
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives

*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
NPO29509	Leucetta chagosensis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193030]
NPO29509	Leucetta chagosensis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165143]
NPO29509	Leucetta chagosensis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17822294]
NPO25094	Artemisia princeps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17996677]
NPO29473	Amycolatopsis mediterranei	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25256628]
NPO644	Pestalotiopsis theae	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27731995]
NPO29509	Leucetta chagosensis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	PMID[29648818]
NPO29255	Salvia chinensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30370766]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25094	Artemisia princeps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25094	Artemisia princeps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25094	Artemisia princeps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28861	Cladonia graciliformis	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25094	Artemisia princeps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29509	Leucetta chagosensis	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28968	Teucrium flavum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29434	Centaurea involucrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29255	Salvia chinensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29238	Heterocondylus vitalbae	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17683	Cryptocarya moschata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29473	Amycolatopsis mediterranei	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29124	Argemone squarrosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24421.1	Agave salmiana var. ferox	Varieties	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29065	Hypoxis rooperi	Species	Hypoxidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29470	Anhalonium fissuratum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO644	Pestalotiopsis theae	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29025	Streptomyces nojiriensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29043	Hypoxylon oceanicum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24342	Lupinus albus	Species	Fabaceae	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 NPC92193 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	449
0.1-0.2	4464
0.2-0.3	12771
0.3-0.4	14072
0.4-0.5	6559
0.5-0.6	3479
0.6-0.7	845
0.7-0.8	54
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	1

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 NPC92193 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	226
0.1-0.2	686
0.2-0.3	776
0.3-0.4	1274
0.4-0.5	2789
0.5-0.6	2366
0.6-0.7	962
0.7-0.8	71
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