NPASS Compound

Structure

NPC242839 OpenBabel06302215142D 35 38 0 0 1 0 0 0 0 0999 V2000 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 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 -0.8660 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 -1.7321 3.0000 0.0000 C 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 -2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 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 -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 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 -6.0622 0.5000 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 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 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 1 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 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 1 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 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 -1.0000 0.0000 O 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 -0.0000 -0.0000 0.0000 O 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 -1.5000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 21 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 23 1 0 0 0 0 5 6 1 0 0 0 0 6 20 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 21 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 20 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 19 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 21 22 1 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 24 32 1 0 0 0 0 25 26 1 0 0 0 0 25 35 1 6 0 0 0 26 27 1 0 0 0 0 26 34 1 1 0 0 0 27 28 1 0 0 0 0 27 33 1 6 0 0 0 28 29 1 1 0 0 0 28 32 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.36
Volume:	514.542
LogP:	5.662
LogD:	4.506
LogS:	-4.369
# Rotatable Bonds:	1
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.397
Synthetic Accessibility Score:	4.795
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.243
MDCK Permeability:	2.2238769815885462e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.276
30% Bioavailability (F30%):	0.689

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.638
Plasma Protein Binding (PPB):	92.28779602050781%
Volume Distribution (VD):	0.623
Pgp-substrate:	7.55689811706543%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.165
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.846
CYP2C9-inhibitor:	0.149
CYP2C9-substrate:	0.927
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.231
CYP3A4-inhibitor:	0.256
CYP3A4-substrate:	0.159

ADMET: Excretion

Clearance (CL):	2.757
Half-life (T1/2):	0.178

ADMET: Toxicity

hERG Blockers:	0.109
Human Hepatotoxicity (H-HT):	0.158
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.982
Maximum Recommended Daily Dose:	0.995
Skin Sensitization:	0.828
Carcinogencity:	0.172
Eye Corrosion:	0.092
Eye Irritation:	0.417
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: NPC242839

Natural Product ID:	NPC242839
*Common Name:**	UWBKEKWTUMGDCN-QSUZLTIMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UWBKEKWTUMGDCN-QSUZLTIMSA-N
Standard InCHI:	InChI=1S/C22H20O13/c1-32-19-13(34-22-18(29)16(27)17(28)20(35-22)21(30)31)6-12-14(15(19)26)10(25)5-11(33-12)7-2-3-8(23)9(24)4-7/h2-6,16-18,20,22-24,26-29H,1H3,(H,30,31)/t16-,17-,18+,20-,22+/m0/s1
SMILES:	COc1c(cc2c(c(=O)cc(c3ccc(c(c3)O)O)o2)c1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	158227
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0002934] Flavonoid O-glucuronides [CHEMONTID:0003534] Flavonoid-7-O-glucuronides

*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
NPO1786	Pyrus pyrifolia	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19162	Tsuga heterophylla	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1786	Pyrus pyrifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7527	Isodon leucophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17106	Phyllanthus discoides	Species	Leiothrichidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18920	Hexalobus crispiflorus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1786	Pyrus pyrifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17106	Phyllanthus discoides	Species	Leiothrichidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7527	Isodon leucophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19162	Tsuga heterophylla	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18920	Hexalobus crispiflorus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17106	Phyllanthus discoides	Species	Leiothrichidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2590	Cordia elaeagnoides	Species	Cordiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18835	Aloe nobilis	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17464	Uncaria sessilifructus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13706	Barleria acanthoides	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19005	Engleromyces goetzei	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO1786	Pyrus pyrifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17205	Laurencia thyrsifera	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19162	Tsuga heterophylla	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22170	Actinoplanes awajinensis	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17106	Phyllanthus discoides	Species	Leiothrichidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19430	Chondrococcus hornemanni	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO16763	Marrubium globosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7566	Ptelea viscosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18920	Hexalobus crispiflorus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO290	Gibberella lateritium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7527	Isodon leucophyllus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19509	Euodia lunu-ankenda	Species	Rutaceae	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 NPC242839 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	417
0.1-0.2	1848
0.2-0.3	4288
0.3-0.4	9502
0.4-0.5	8435
0.5-0.6	4348
0.6-0.7	5287
0.7-0.8	5264
0.8-0.85	1643
0.85-0.9	1088
0.9-0.95	404
0.95-1	173

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 NPC242839 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	386
0.1-0.2	966
0.2-0.3	2024
0.3-0.4	2651
0.4-0.5	1782
0.5-0.6	884
0.6-0.7	286
0.7-0.8	128
0.8-0.85	18
0.85-0.9	17
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