NPASS Compound

Structure

NPC102803 OpenBabel06302215132D 31 34 0 0 1 0 0 0 0 0999 V2000 5.1962 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 1 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 2 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 1.7321 0.0000 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 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 O 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 3.4641 3.0000 0.0000 C 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 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 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 0.8660 2.5000 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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 31 1 6 0 0 0 4 5 1 0 0 0 0 4 30 1 1 0 0 0 5 6 1 0 0 0 0 5 29 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 19 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 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 13 28 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 27 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 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 26 1 0 0 0 0 24 25 1 0 0 0 0 M CHG 1 26 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.11
Volume:	404.357
LogP:	2.077
LogD:	1.331
LogS:	-3.912
# Rotatable Bonds:	3
TPSA:	170.05
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.348
Synthetic Accessibility Score:	3.883
Fsp3:	0.286
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:	-6.184
MDCK Permeability:	6.891035809530877e-06
Pgp-inhibitor:	0.009
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.254
20% Bioavailability (F20%):	0.109
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	92.30927276611328%
Volume Distribution (VD):	0.785
Pgp-substrate:	8.378283500671387%

ADMET: Metabolism

CYP1A2-inhibitor:	0.706
CYP1A2-substrate:	0.071
CYP2C19-inhibitor:	0.053
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.331
CYP2C9-substrate:	0.839
CYP2D6-inhibitor:	0.563
CYP2D6-substrate:	0.188
CYP3A4-inhibitor:	0.485
CYP3A4-substrate:	0.026

ADMET: Excretion

Clearance (CL):	6.434
Half-life (T1/2):	0.784

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.091
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.782
Rat Oral Acute Toxicity:	0.102
Maximum Recommended Daily Dose:	0.039
Skin Sensitization:	0.758
Carcinogencity:	0.127
Eye Corrosion:	0.003
Eye Irritation:	0.53
Respiratory Toxicity:	0.073

Download Data

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

Natural Product: NPC102803

Natural Product ID:	NPC102803
*Common Name:**	SOSLMHZOJATCCP-MKMJNHTISA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SOSLMHZOJATCCP-MKMJNHTISA-M
Standard InCHI:	InChI=1S/C21H20O10/c1-8-15(25)17(27)18(28)21(29-8)31-20-16(26)14-12(24)6-11(23)7-13(14)30-19(20)9-2-4-10(22)5-3-9/h2-8,15,17-18,21-25,27-28H,1H3/p-1/t8-,15-,17+,18+,21+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(cc1)[O-])O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25202794
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-glycosides

*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
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(01)00320-X]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1021/np50070a005]
NPO12458	Zingiber aromaticum	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	DOI[10.1080/10575639708043725]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11738417]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754604]
NPO12458	Zingiber aromaticum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15270556]
NPO15704	Euphorbia lunulata	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[15744103]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	root	n.a.	PMID[18975262]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	Roots	Simao city, Yunnan Province, China	2007-MAY	PMID[19374435]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	bark	n.a.	n.a.	PMID[20045319]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	leaves	Botanical Garden of Innsbruck, Austria	n.a.	PMID[20100662]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21443171]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21462031]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21923134]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24333010]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26341132]
NPO1436	Houttuynia cordata	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29099182]
NPO20518	Polygala chinensis	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22819	Rodgersia podophylla	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2724.1	Excoecaria cochinchinensis var. viridis	Varieties	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12458	Zingiber aromaticum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13782	Dicranopteris pedata	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15704	Euphorbia lunulata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1436	Houttuynia cordata	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20518	Polygala chinensis	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22819	Rodgersia podophylla	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2724.1	Excoecaria cochinchinensis var. viridis	Varieties	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15704	Euphorbia lunulata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13782	Dicranopteris pedata	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12458	Zingiber aromaticum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1436	Houttuynia cordata	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1436	Houttuynia cordata	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15704	Euphorbia lunulata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20518	Polygala chinensis	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1436	Houttuynia cordata	Species	Saururaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18176	Ephedra sinica	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25618	Eriobotrya japonica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13782	Dicranopteris pedata	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15361	Alnus japonica	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20518	Polygala chinensis	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22819	Rodgersia podophylla	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15704	Euphorbia lunulata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12458	Zingiber aromaticum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18176	Ephedra sinica	Species	Ephedraceae	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 NPC102803 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	407
0.1-0.2	1724
0.2-0.3	4072
0.3-0.4	9705
0.4-0.5	8599
0.5-0.6	4492
0.6-0.7	5714
0.7-0.8	4682
0.8-0.85	2069
0.85-0.9	708
0.9-0.95	389
0.95-1	136

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 NPC102803 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	377
0.1-0.2	911
0.2-0.3	1828
0.3-0.4	2729
0.4-0.5	1894
0.5-0.6	962
0.6-0.7	277
0.7-0.8	127
0.8-0.85	23
0.85-0.9	14
0.9-0.95	8
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