NPASS Compound

Structure

NPC294731 OpenBabel06302215142D 35 39 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 1 0 0 0 3 4 1 0 0 0 0 3 16 1 0 0 0 0 4 5 1 0 0 0 0 5 14 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 34 1 0 0 0 0 11 12 2 0 0 0 0 11 32 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 17 18 1 0 0 0 0 18 27 2 0 0 0 0 18 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 30 1 0 0 0 0 22 23 2 0 0 0 0 22 28 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 32 33 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	476.27
Volume:	503.42
LogP:	4.906
LogD:	4.18
LogS:	-4.64
# Rotatable Bonds:	7
TPSA:	53.05
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	3.665
Fsp3:	0.483
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.373
MDCK Permeability:	2.946483982668724e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.561
30% Bioavailability (F30%):	0.46

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.141
Plasma Protein Binding (PPB):	76.14997100830078%
Volume Distribution (VD):	1.571
Pgp-substrate:	3.946868658065796%

ADMET: Metabolism

CYP1A2-inhibitor:	0.079
CYP1A2-substrate:	0.965
CYP2C19-inhibitor:	0.356
CYP2C19-substrate:	0.953
CYP2C9-inhibitor:	0.097
CYP2C9-substrate:	0.679
CYP2D6-inhibitor:	0.271
CYP2D6-substrate:	0.94
CYP3A4-inhibitor:	0.771
CYP3A4-substrate:	0.935

ADMET: Excretion

Clearance (CL):	8.582
Half-life (T1/2):	0.495

ADMET: Toxicity

hERG Blockers:	0.943
Human Hepatotoxicity (H-HT):	0.527
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.14
Rat Oral Acute Toxicity:	0.381
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.586
Carcinogencity:	0.038
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.86

Download Data

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

Natural Product: NPC294731

Natural Product ID:	NPC294731
*Common Name:**	MBYXEBXZARTUSS-HMHJJOSWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MBYXEBXZARTUSS-HMHJJOSWSA-N
Standard InCHI:	InChI=1S/C29H36N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h7,9,13-16,18,21,25H,6,8,10-12,17H2,1-5H3/t18-,21-,25-/m0/s1
SMILES:	CC[C@H]1CN2CCc3cc(c(cc3[C@@H]2C[C@@H]1Cc1c2cc(c(cc2ccn1)OC)OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	442217
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000221] Quinolizidines

*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
NPO2719	Amauroascus aureus	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5735362]
NPO24848	Acodontaster conspicuus	Species	Odontasteridae	Eukaryota	n.a.	Antarctic	n.a.	PMID[9358635]
NPO24728	Tragopogon porrifolius	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO24728	Tragopogon porrifolius	Species	Asteraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24728	Tragopogon porrifolius	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23138	Swainsona salsula	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24728	Tragopogon porrifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26637.1	Mentha aquatica var. citrata	Varieties	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25360	Helminthosporium ravenelii	Species	Massarinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25098	Spinacia glabra	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25409	Ascochyta caulina	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2690	Carapichea ipecacuanha	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24521	Helichrysum revolutum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24211	Parmelia cetrarioides	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24880	Bacterial str	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23138	Swainsona salsula	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24728	Tragopogon porrifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24646	Coryphantha elephantidens	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23623	Hirsutella nivea	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5056	Helichrysum heterolasium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18432	Poria corticola	Species	Coccinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2719	Amauroascus aureus	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24848	Acodontaster conspicuus	Species	Odontasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26128	Clonostachys rosea	Species	Bionectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22548	Osteospermum jucundum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21010	Streptomyces avidinii	Species	Streptomycetaceae	Bacteria	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 NPC294731 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	608
0.1-0.2	2831
0.2-0.3	13730
0.3-0.4	4801
0.4-0.5	13734
0.5-0.6	4429
0.6-0.7	2196
0.7-0.8	303
0.8-0.85	37
0.85-0.9	21
0.9-0.95	7
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 NPC294731 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	315
0.1-0.2	614
0.2-0.3	922
0.3-0.4	1266
0.4-0.5	2645
0.5-0.6	2223
0.6-0.7	972
0.7-0.8	180
0.8-0.85	8
0.85-0.9	3
0.9-0.95	2
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