NPASS Compound

Structure

NPC93953 OpenBabel06302215512D 27 29 0 0 1 0 0 0 0 0999 V2000 2.7266 -2.8955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5926 -2.3955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5926 -1.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7266 -0.8955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7266 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5926 0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4586 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4586 -0.8955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3246 -1.3955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8605 0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9945 0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2079 -0.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1215 -1.3849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2260 -2.3794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1395 -2.7861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9485 -2.1984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8440 -1.2038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9305 -0.7971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6530 -0.6161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5485 0.3785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8621 -2.6051 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6691 0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6473 0.5352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9945 1.1045 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 11 1 0 0 0 0 11 24 1 0 0 0 0 11 12 1 0 0 0 0 11 27 1 6 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 6 0 0 0 14 24 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 24 25 1 1 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	376.15
Volume:	374.52
LogP:	1.355
LogD:	1.549
LogS:	-2.67
# Rotatable Bonds:	6
TPSA:	108.61
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.608
Synthetic Accessibility Score:	3.656
Fsp3:	0.4
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:	-5.139
MDCK Permeability:	5.475374109664699e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.887
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.158
30% Bioavailability (F30%):	0.423

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.154
Plasma Protein Binding (PPB):	89.13658905029297%
Volume Distribution (VD):	1.293
Pgp-substrate:	14.444443702697754%

ADMET: Metabolism

CYP1A2-inhibitor:	0.048
CYP1A2-substrate:	0.636
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.545
CYP2C9-inhibitor:	0.111
CYP2C9-substrate:	0.665
CYP2D6-inhibitor:	0.191
CYP2D6-substrate:	0.822
CYP3A4-inhibitor:	0.784
CYP3A4-substrate:	0.6

ADMET: Excretion

Clearance (CL):	13.71
Half-life (T1/2):	0.868

ADMET: Toxicity

hERG Blockers:	0.087
Human Hepatotoxicity (H-HT):	0.314
Drug-inuced Liver Injury (DILI):	0.071
AMES Toxicity:	0.427
Rat Oral Acute Toxicity:	0.045
Maximum Recommended Daily Dose:	0.131
Skin Sensitization:	0.303
Carcinogencity:	0.19
Eye Corrosion:	0.003
Eye Irritation:	0.192
Respiratory Toxicity:	0.044

Download Data

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

Natural Product: NPC93953

Natural Product ID:	NPC93953
*Common Name:**	BVHIKUCXNBQDEM-JSNMRZPZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BVHIKUCXNBQDEM-JSNMRZPZSA-N
Standard InCHI:	InChI=1S/C20H24O7/c1-25-17-7-12(3-5-15(17)22)9-20(24)11-27-19(14(20)10-21)13-4-6-16(23)18(8-13)26-2/h3-8,14,19,21-24H,9-11H2,1-2H3/t14-,19-,20-/m1/s1
SMILES:	COc1cc(ccc1O)C[C@]1(CO[C@H](c2ccc(c(c2)OC)O)[C@H]1CO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5273570
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003422] 7,9'-epoxylignans

*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
NPO19975	Pycnandra acuminata	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytochem.2007.07.001]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	seeds	n.a.	n.a.	PMID[12762787]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762809]
NPO6412	Echinacea pallida	Species	Asteraceae	Eukaryota	root	n.a.	n.a.	PMID[15921428]
NPO1743	Neurospora terricola	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19795843]
NPO12498	Carpesium cernuum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27668963]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11886	Hemerocallis citrina	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11886	Hemerocallis citrina	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4322	Scabiosa succisa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20569	Psychotria serpens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1743	Neurospora terricola	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO633	Mesembryanthemum expansum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5534	Alternaria kikuchiana	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19975	Pycnandra acuminata	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12498	Carpesium cernuum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1695	Monascus pilosus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6514	Desmotrichum fimbriatum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5140	Dipteryx odorata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9871.1	Ficus benghalensis var. krishnae	Varieties	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6412	Echinacea pallida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12736	Galleria mellonella	Species	Pyralidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12118	Cleistopholis staudtii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10825	Nerine sarniensis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11339	Litsea salicifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8609	Hopea utilis	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12602	Leuzea centauroides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9577	Triclisia dictyophylla	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO940	Vernonia anisochaetoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11886	Hemerocallis citrina	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12828	Dysidea tupha	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6012	Dumoria heckelii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4759	Helleborus multifidus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6861	Galium dasypodum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10010	Evernia vulpina	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10970	Osmorhiza aristata	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO218	Acer carpinifolium	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO35	Zanthoxylum dinklagei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8129	Inocybe geophylla	Species	Inocybaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11506	Stipa vaseyi	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10298	Symbiodinium microadriaticum	Species	Symbiodiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7874	Helichrysum lepidissimum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26095	Hypericum revolutum	Species	Hypericaceae	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 NPC93953 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	375
0.1-0.2	1221
0.2-0.3	3311
0.3-0.4	8918
0.4-0.5	10128
0.5-0.6	4675
0.6-0.7	9272
0.7-0.8	3409
0.8-0.85	810
0.85-0.9	438
0.9-0.95	104
0.95-1	36

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 NPC93953 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	296
0.1-0.2	764
0.2-0.3	1690
0.3-0.4	2639
0.4-0.5	1909
0.5-0.6	1036
0.6-0.7	658
0.7-0.8	150
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
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