NPASS Compound

Structure

NPC116391 OpenBabel06302215422D 32 35 0 0 1 0 0 0 0 0999 V2000 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 1.7321 -2.0000 0.0000 C 0 0 1 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 -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 0.0000 -3.0000 0.0000 C 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 -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 0.0000 -2.0000 0.0000 C 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 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 -2.5981 -1.5000 0.0000 O 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 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 32 1 0 0 0 0 4 5 2 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 17 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 29 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 15 1 1 0 0 0 18 19 1 0 0 0 0 18 25 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 6 0 0 0 20 21 1 0 0 0 0 20 27 1 1 0 0 0 21 22 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 1 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.12
Volume:	415.784
LogP:	0.283
LogD:	0.019
LogS:	-3.777
# Rotatable Bonds:	3
TPSA:	197.37
# H-Bond Aceptor:	11
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.287
Synthetic Accessibility Score:	4.309
Fsp3:	0.381
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.53
MDCK Permeability:	4.147268100496149e-06
Pgp-inhibitor:	0.013
Pgp-substrate:	0.719
Human Intestinal Absorption (HIA):	0.841
20% Bioavailability (F20%):	0.895
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.033
Plasma Protein Binding (PPB):	88.01891326904297%
Volume Distribution (VD):	0.753
Pgp-substrate:	15.591108322143555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.048
CYP1A2-substrate:	0.034
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.12
CYP2C9-substrate:	0.451
CYP2D6-inhibitor:	0.045
CYP2D6-substrate:	0.172
CYP3A4-inhibitor:	0.078
CYP3A4-substrate:	0.052

ADMET: Excretion

Clearance (CL):	7.039
Half-life (T1/2):	0.763

ADMET: Toxicity

hERG Blockers:	0.183
Human Hepatotoxicity (H-HT):	0.271
Drug-inuced Liver Injury (DILI):	0.968
AMES Toxicity:	0.701
Rat Oral Acute Toxicity:	0.562
Maximum Recommended Daily Dose:	0.166
Skin Sensitization:	0.936
Carcinogencity:	0.229
Eye Corrosion:	0.003
Eye Irritation:	0.789
Respiratory Toxicity:	0.061

Download Data

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

Natural Product: NPC116391

Natural Product ID:	NPC116391
*Common Name:**	CMVYWFJFAHQVQP-PFGOOLOPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CMVYWFJFAHQVQP-PFGOOLOPSA-N
Standard InCHI:	InChI=1S/C21H22O11/c22-6-14-17(28)18(29)19(30)21(32-14)16-11(26)4-10(25)15-12(27)5-13(31-20(15)16)7-1-2-8(23)9(24)3-7/h1-4,13-14,17-19,21-26,28-30H,5-6H2/t13-,14-,17-,18+,19-,21+/m1/s1
SMILES:	c1cc(c(cc1[C@H]1CC(=O)c2c(cc(c(c2O1)[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	134715223
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001737] Flavonoid C-glycosides [CHEMONTID:0003535] Flavonoid 8-C-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
NPO27025	Erylus trisphaerus	Species	Geodiidae	Eukaryota	n.a.	Dominican	n.a.	PMID[12713417]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	New Caledonia	n.a.	PMID[15652581]
NPO26969	Sagittaria sagittifolia	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499326]
NPO27576	Lysiana subfalcata	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18222087]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1955887]
NPO19202	Phaeolus schweinitzii	Species	Hymenochaetaceae	Eukaryota	fruits	Tibetan Plateau	n.a.	PMID[23869482]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2878063]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7130988]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	bark	n.a.	n.a.	PMID[7623034]
NPO26969	Sagittaria sagittifolia	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27675	Platycarya strobilacea	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27237	Aucuba chinensis	Species	Garryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27376	Curculigo pilosa	Species	Hypoxidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27640	Sorbus tianschanica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27840	Stephania elegans	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27675	Platycarya strobilacea	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9698	Parablechnum minus	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26969	Sagittaria sagittifolia	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27640	Sorbus tianschanica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27376	Curculigo pilosa	Species	Hypoxidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27612	Peperomia vulcanica	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26969	Sagittaria sagittifolia	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27675	Platycarya strobilacea	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27640	Sorbus tianschanica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19202	Phaeolus schweinitzii	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27800	Usnea undulata	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27312	Citrus tangerina	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27696	Anolis lineatopus	Species	Iguanidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27440	Osteospermum muricatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27612	Peperomia vulcanica	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19173	Gleditsia caspica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15795	Humata pectinata	Species	Davalliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27597	Haplophyllum ramosissimum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9698	Parablechnum minus	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27788	Eupatorium areolare	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27470	Centaurea huber-morathii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27274	Amsinckia tessellata	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27138	Entada rheedei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27394	Sideritis euboea	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27525	Saussurea amara	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26882	Swertia swertopsis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22520	Felimida luteorosea	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27290	Carica dodecaphylla	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25349	Bistorta vivipara	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27453	Trichoderma koningi	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27237	Aucuba chinensis	Species	Garryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27419	Aurelia aurita	Species	Ulmaridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27076	Aspergillus mutabilis	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27761	Aspalathus linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27732	Cynometra lujae	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27254	Utricularia australis	Species	Lentibulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26912	Premna tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27064	Taxus brevifolia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14449	Cedronella canariensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6917	Kali turgidum	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27495	Sisyrinchium californicum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27345	Crocus minimus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26969	Sagittaria sagittifolia	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15868	0stoc spongiaeforme	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18100	Physalis edulis	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29241	Macaranga peltata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27675	Platycarya strobilacea	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27576	Lysiana subfalcata	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27215	Gracilaria textorii	Species	Gracilariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27025	Erylus trisphaerus	Species	Geodiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27099	Virgilia divaricata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27840	Stephania elegans	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27815	Sia ferox	Species	Stenopelmatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27376	Curculigo pilosa	Species	Hypoxidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27050	Tsuga chinensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27712	Helichrysum mixtum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29217	Brickellia vernicosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27640	Sorbus tianschanica	Species	Rosaceae	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 NPC116391 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	430
0.1-0.2	1609
0.2-0.3	3729
0.3-0.4	9702
0.4-0.5	8724
0.5-0.6	3625
0.6-0.7	4772
0.7-0.8	5553
0.8-0.85	2851
0.85-0.9	1460
0.9-0.95	235
0.95-1	7

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 NPC116391 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	383
0.1-0.2	858
0.2-0.3	1799
0.3-0.4	2617
0.4-0.5	1836
0.5-0.6	1019
0.6-0.7	452
0.7-0.8	135
0.8-0.85	32
0.85-0.9	14
0.9-0.95	5
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