NPASS Compound

Structure

NPC14359 OpenBabel06302215202D 31 34 0 0 0 0 0 0 0 0999 V2000 0.8660 3.5000 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 1.7321 2.0000 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 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 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 2.5981 -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 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 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 0.0000 -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 O 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 -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 C 0 0 0 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 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 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 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 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 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 2 0 0 0 0 5 6 1 0 0 0 0 6 13 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 13 1 0 0 0 0 14 15 2 0 0 0 0 14 30 1 0 0 0 0 15 29 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 28 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	767.35
Volume:	777.098
LogP:	3.796
LogD:	2.303
LogS:	-4.329
# Rotatable Bonds:	16
TPSA:	178.11
# H-Bond Aceptor:	14
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.186
Synthetic Accessibility Score:	6.227
Fsp3:	0.585
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.237
MDCK Permeability:	0.00023317513114307076
Pgp-inhibitor:	1.0
Pgp-substrate:	0.977
Human Intestinal Absorption (HIA):	0.345
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.909

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	47.76340866088867%
Volume Distribution (VD):	1.973
Pgp-substrate:	36.84149169921875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.012
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.092
CYP2C9-inhibitor:	0.099
CYP2C9-substrate:	0.009
CYP2D6-inhibitor:	0.723
CYP2D6-substrate:	0.067
CYP3A4-inhibitor:	0.395
CYP3A4-substrate:	0.628

ADMET: Excretion

Clearance (CL):	3.379
Half-life (T1/2):	0.019

ADMET: Toxicity

hERG Blockers:	0.088
Human Hepatotoxicity (H-HT):	0.988
Drug-inuced Liver Injury (DILI):	0.945
AMES Toxicity:	0.026
Rat Oral Acute Toxicity:	0.483
Maximum Recommended Daily Dose:	0.538
Skin Sensitization:	0.082
Carcinogencity:	0.038
Eye Corrosion:	0.004
Eye Irritation:	0.012
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC14359

Natural Product ID:	NPC14359
*Common Name:**	GVACMMPZGMSLAB-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GVACMMPZGMSLAB-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H24O6/c1-13(2)5-7-16-23-15(9-10-25(3,4)31-23)22(29)21-19(28)12-20(30-24(16)21)14-6-8-17(26)18(27)11-14/h5-6,8-12,26-27,29H,7H2,1-4H3
SMILES:	CC(=CCc1c2c(C=CC(C)(C)O2)c(c2c(=O)cc(c3ccc(c(c3)O)O)oc12)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0003504] 8-prenylated flavones

*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
NPO3973	Flammulina velutipes	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473426]
NPO13341	Bryopsis pennata	Species	Bryopsidaceae	Eukaryota	n.a.	Hawaiian	n.a.	PMID[19916528]
NPO3973	Flammulina velutipes	Species	Physalacriaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17479	Aconitum tanguticum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17479	Aconitum tanguticum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27048	Pyropia tenera	Species	Bangiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27048	Pyropia tenera	Species	Bangiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17344	Strychnos henningsii	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3026	Strophanthus hispidus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18809	Lyophyllum connatum	Species	Lyophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18724	Polyalthia stenopetala	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13451	Pseudotsuga japonica	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18218	Acanthophyllum sordidum	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12356	Aphelandra chamissoniana	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3973	Flammulina velutipes	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10468	Ficus beecheyana	Species	Ficidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27114	Aconitum habaense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13834	Lecidea carpathica	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17479	Aconitum tanguticum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19389	Roemeria refracta	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19586	Bougainvillea glabra	Species	Nyctaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26105	Panax spinosus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13341	Bryopsis pennata	Species	Bryopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18478	Vernonia scorpioides	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 NPC14359 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	444
0.1-0.2	1827
0.2-0.3	4475
0.3-0.4	10985
0.4-0.5	6857
0.5-0.6	3634
0.6-0.7	5088
0.7-0.8	4777
0.8-0.85	2252
0.85-0.9	1620
0.9-0.95	692
0.95-1	46

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 NPC14359 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	397
0.1-0.2	982
0.2-0.3	1705
0.3-0.4	2688
0.4-0.5	1820
0.5-0.6	1015
0.6-0.7	364
0.7-0.8	115
0.8-0.85	45
0.85-0.9	12
0.9-0.95	7
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