NPASS Compound

Structure

NPC189297 OpenBabel06302215562D 24 26 0 0 0 0 0 0 0 0999 V2000 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 O 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 -2.5981 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 -4.3301 -1.5000 0.0000 O 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 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 1.7321 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 2.5981 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 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 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 20 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 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 15 24 1 0 0 0 0 16 17 1 0 0 0 0 16 23 1 0 0 0 0 17 18 2 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.07
Volume:	317.359
LogP:	2.968
LogD:	2.46
LogS:	-3.904
# Rotatable Bonds:	3
TPSA:	109.36
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.633
Synthetic Accessibility Score:	2.481
Fsp3:	0.118
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.964
MDCK Permeability:	1.2527450962807052e-05
Pgp-inhibitor:	0.131
Pgp-substrate:	0.096
Human Intestinal Absorption (HIA):	0.1
20% Bioavailability (F20%):	0.019
30% Bioavailability (F30%):	0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	91.17906188964844%
Volume Distribution (VD):	0.775
Pgp-substrate:	13.372397422790527%

ADMET: Metabolism

CYP1A2-inhibitor:	0.935
CYP1A2-substrate:	0.951
CYP2C19-inhibitor:	0.139
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.699
CYP2C9-substrate:	0.817
CYP2D6-inhibitor:	0.23
CYP2D6-substrate:	0.742
CYP3A4-inhibitor:	0.299
CYP3A4-substrate:	0.182

ADMET: Excretion

Clearance (CL):	7.464
Half-life (T1/2):	0.868

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.126
Drug-inuced Liver Injury (DILI):	0.969
AMES Toxicity:	0.569
Rat Oral Acute Toxicity:	0.079
Maximum Recommended Daily Dose:	0.448
Skin Sensitization:	0.893
Carcinogencity:	0.194
Eye Corrosion:	0.003
Eye Irritation:	0.72
Respiratory Toxicity:	0.343

Download Data

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

Natural Product: NPC189297

Natural Product ID:	NPC189297
*Common Name:**	ZHIWPTGNBDHONL-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZHIWPTGNBDHONL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C17H14O7/c1-22-13-5-8(3-4-9(13)18)12-6-10(19)15-16(21)11(20)7-14(23-2)17(15)24-12/h3-7,18,20-21H,1-2H3
SMILES:	COc1cc(ccc1O)c1cc(=O)c2c(c(cc(c2o1)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15429100
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002593] 8-O-methylated flavonoids

*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
NPO11960	Myriastra clavosa	Species	n.a.	n.a.	n.a.	Philippines	n.a.	PMID[12193033]
NPO11960	Myriastra clavosa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[12350152]
NPO15105	Lyngbya semiplena	Species	Oscillatoriaceae	Bacteria	n.a.	Papua New Guinea	n.a.	PMID[14575438]
NPO1762	Citropsis articulata	Species	Rutaceae	Eukaryota	n.a.	root	n.a.	PMID[21985060]
NPO1762	Citropsis articulata	Species	Rutaceae	Eukaryota	Root Bark	n.a.	n.a.	PMID[21985060]
NPO19302	Amathia alternata	Species	Vesiculariidae	Eukaryota	n.a.	Atlantic	n.a.	PMID[9249973]
NPO12968	Crotalaria spectabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12968	Crotalaria spectabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25840	Sargassum fusiforme	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25840	Sargassum fusiforme	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25840	Sargassum fusiforme	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12968	Crotalaria spectabilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19302	Amathia alternata	Species	Vesiculariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18035	Lagerstroemia flos-reginae	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19079	Vatica pauciflora	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22538	Dendrobium plicatile	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15105	Lyngbya semiplena	Species	Oscillatoriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16082	Flindersia bennettiana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1762	Citropsis articulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13312	Senecio panduriformis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10039	Podosphaera fuliginea	Species	Erysiphaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14198	Haliclona valliculata	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17744	Litsea elliptica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11960	Myriastra clavosa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14705	Tanacetopsis mucronata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19237	Sargassum macrocarpum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18258	Zanthoxylum rhoifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18669	Myriophyllum verticillatum	Species	Haloragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13667	Manoao colensoi	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11070	Nervilia purpurea	Species	Orchidaceae	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 NPC189297 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	480
0.1-0.2	2045
0.2-0.3	5283
0.3-0.4	11455
0.4-0.5	5595
0.5-0.6	4083
0.6-0.7	5142
0.7-0.8	4776
0.8-0.85	1856
0.85-0.9	1104
0.9-0.95	612
0.95-1	266

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 NPC189297 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	450
0.1-0.2	1006
0.2-0.3	1906
0.3-0.4	2679
0.4-0.5	1673
0.5-0.6	954
0.6-0.7	332
0.7-0.8	96
0.8-0.85	34
0.85-0.9	11
0.9-0.95	6
0.95-1	3

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