NPASS Compound

Structure

NPC157894 OpenBabel06302216002D 26 29 0 0 0 0 0 0 0 0999 V2000 5.7608 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1730 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 -2.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -2.9271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1730 -2.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5797 -3.0316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5743 -3.1361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1620 -2.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7553 -1.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7608 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7608 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3431 -0.6045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3376 -0.7091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1566 -2.4316 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 20 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 26 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 24 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 23 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 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	355.14
Volume:	356.743
LogP:	2.852
LogD:	2.777
LogS:	-3.976
# Rotatable Bonds:	1
TPSA:	68.23
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.848
Synthetic Accessibility Score:	3.129
Fsp3:	0.35
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.955
MDCK Permeability:	2.303168184880633e-05
Pgp-inhibitor:	0.026
Pgp-substrate:	0.05
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.975
Plasma Protein Binding (PPB):	89.32291412353516%
Volume Distribution (VD):	1.81
Pgp-substrate:	9.21072769165039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.936
CYP1A2-substrate:	0.804
CYP2C19-inhibitor:	0.584
CYP2C19-substrate:	0.817
CYP2C9-inhibitor:	0.04
CYP2C9-substrate:	0.579
CYP2D6-inhibitor:	0.964
CYP2D6-substrate:	0.899
CYP3A4-inhibitor:	0.888
CYP3A4-substrate:	0.816

ADMET: Excretion

Clearance (CL):	18.017
Half-life (T1/2):	0.495

ADMET: Toxicity

hERG Blockers:	0.547
Human Hepatotoxicity (H-HT):	0.296
Drug-inuced Liver Injury (DILI):	0.881
AMES Toxicity:	0.133
Rat Oral Acute Toxicity:	0.448
Maximum Recommended Daily Dose:	0.227
Skin Sensitization:	0.528
Carcinogencity:	0.558
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.777

Download Data

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

Natural Product: NPC157894

Natural Product ID:	NPC157894
*Common Name:**	JUQBPFGIFICIIN-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JUQBPFGIFICIIN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H21NO5/c1-21-6-5-13-8-18-19(26-11-25-18)9-14(13)17(23)7-12-3-4-16(22)20(24-2)15(12)10-21/h3-4,8-9,22H,5-7,10-11H2,1-2H3
SMILES:	CN1CCc2cc3c(cc2C(=O)Cc2ccc(c(c2C1)OC)O)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5321910
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002743] Protopine 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
NPO20958	Smenospongia aurea	Species	Thorectidae	Eukaryota	n.a.	Jamaican	n.a.	PMID[11975483]
NPO20254	Ipomoea leptophylla	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14640518]
NPO22556	Dendrolobium lanceolatum	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[15217275]
NPO927	Swertia mussotii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19645233]
NPO927	Swertia mussotii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO927	Swertia mussotii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2114.1	Thalictrum minus var. hypoleucum	Varieties	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO927	Swertia mussotii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2114.1	Thalictrum minus var. hypoleucum	Varieties	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14326	Pseudocercospora fijiensis	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22556	Dendrolobium lanceolatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21026	Pericopsis mooniana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20958	Smenospongia aurea	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17360	Argemone albiflora	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22817	Actinidia valvata	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2114.1	Thalictrum minus var. hypoleucum	Varieties	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20254	Ipomoea leptophylla	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18680	Larix decidua	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21848	Rosa hybr	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22495	Cladonia alpestris	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18257	Oberna wallichiana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO927	Swertia mussotii	Species	Gentianaceae	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 NPC157894 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	274
0.1-0.2	1417
0.2-0.3	4953
0.3-0.4	12280
0.4-0.5	4354
0.5-0.6	8300
0.6-0.7	9984
0.7-0.8	1069
0.8-0.85	54
0.85-0.9	5
0.9-0.95	5
0.95-1	2

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 NPC157894 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	705
0.2-0.3	1097
0.3-0.4	1986
0.4-0.5	2574
0.5-0.6	1776
0.6-0.7	724
0.7-0.8	93
0.8-0.85	3
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