NPASS Compound

Structure

NPC284552 OpenBabel06302215162D 26 28 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 -2.5981 -2.5000 0.0000 O 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 -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 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 2.5981 0.5000 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 2.0000 0.0000 C 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 3.4641 2.0000 0.0000 O 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 -0.0000 0.0000 O 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 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 12 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 12 26 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 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 26 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	360.08
Volume:	343.445
LogP:	2.899
LogD:	2.155
LogS:	-3.927
# Rotatable Bonds:	4
TPSA:	118.59
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.65
Synthetic Accessibility Score:	2.554
Fsp3:	0.167
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:	-5.021
MDCK Permeability:	1.4750833543075714e-05
Pgp-inhibitor:	0.97
Pgp-substrate:	0.045
Human Intestinal Absorption (HIA):	0.14
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.293

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	87.2308578491211%
Volume Distribution (VD):	0.728
Pgp-substrate:	23.261842727661133%

ADMET: Metabolism

CYP1A2-inhibitor:	0.815
CYP1A2-substrate:	0.972
CYP2C19-inhibitor:	0.091
CYP2C19-substrate:	0.11
CYP2C9-inhibitor:	0.655
CYP2C9-substrate:	0.749
CYP2D6-inhibitor:	0.145
CYP2D6-substrate:	0.732
CYP3A4-inhibitor:	0.399
CYP3A4-substrate:	0.226

ADMET: Excretion

Clearance (CL):	3.825
Half-life (T1/2):	0.854

ADMET: Toxicity

hERG Blockers:	0.202
Human Hepatotoxicity (H-HT):	0.075
Drug-inuced Liver Injury (DILI):	0.824
AMES Toxicity:	0.237
Rat Oral Acute Toxicity:	0.052
Maximum Recommended Daily Dose:	0.396
Skin Sensitization:	0.906
Carcinogencity:	0.022
Eye Corrosion:	0.004
Eye Irritation:	0.858
Respiratory Toxicity:	0.317

Download Data

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

Natural Product: NPC284552

Natural Product ID:	NPC284552
*Common Name:**	BVRHGBHZAQNORL-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BVRHGBHZAQNORL-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H16O8/c1-23-13-4-8(5-14(24-2)16(13)21)11-6-9(19)15-12(26-11)7-10(20)18(25-3)17(15)22/h4-7,20-22H,1-3H3
SMILES:	COc1cc(cc(c1O)OC)c1cc(=O)c2c(cc(c(c2O)OC)O)o1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14034284
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002591] 6-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
NPO10304	Colletotrichum gloeosporioides	Species	Glomerellaceae	Eukaryota	Artemisia mongolica	n.a.	n.a.	PMID[11087599]
NPO12721	Liriodendron tulipifera	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO10304	Colletotrichum gloeosporioides	Species	Glomerellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29035525]
NPO5118	Zanthoxylum myriacanthum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12721	Liriodendron tulipifera	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1252	Aglaia grandis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26719	Tetrapanax papyrifer	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5118	Zanthoxylum myriacanthum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11452	Pterocarpus officinalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26396	Coprinopsis atramentaria	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12721	Liriodendron tulipifera	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12721	Liriodendron tulipifera	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12153	Adenia globosa	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11452	Pterocarpus officinalis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11583	Calycanthus floridus	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7968	Artemisia kurramensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12721	Liriodendron tulipifera	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10536	Rhabdonia verticillata	Species	Areschougiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7463	Ranzania japonica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10304	Colletotrichum gloeosporioides	Species	Glomerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9447	Tolypothrix tenuis	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO557	Bhesa nitidissima	Species	Centroplacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10081	Othonna sedifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO540	Anaphalis araneosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6802	Rothmannia wittii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7779	Impatiens edgeworthii	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26396	Coprinopsis atramentaria	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26719	Tetrapanax papyrifer	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12613	Catunaregam tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1252	Aglaia grandis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11544	Vernonia lanuginosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10483	Chrysanthemum sinense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5118	Zanthoxylum myriacanthum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10798	Cis punctifer	Species	Ciidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9265	Jasonia candicans	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8120	Episcia cupreata	Species	Gesneriaceae	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 NPC284552 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	457
0.1-0.2	2058
0.2-0.3	5104
0.3-0.4	11626
0.4-0.5	5627
0.5-0.6	3886
0.6-0.7	5058
0.7-0.8	4759
0.8-0.85	2098
0.85-0.9	1132
0.9-0.95	616
0.95-1	276

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 NPC284552 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	442
0.1-0.2	1004
0.2-0.3	1932
0.3-0.4	2665
0.4-0.5	1678
0.5-0.6	939
0.6-0.7	331
0.7-0.8	107
0.8-0.85	32
0.85-0.9	12
0.9-0.95	7
0.95-1	1

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