NPASS Compound

Structure

NPC83341 OpenBabel06302215342D 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 1 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 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 0.1490 -2.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1240 -3.2114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4187 -4.1669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7386 -4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2364 -4.6775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5311 -3.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5283 -3.6472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0917 -2.8209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7969 -1.8653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5300 -1.1852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3074 -0.2102 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 1.0333 -5.8555 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 6 0 0 0 8 9 1 0 0 0 0 9 25 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 23 1 0 0 0 0 11 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 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 28 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 2 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 2 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	430.16
Volume:	424.005
LogP:	1.829
LogD:	1.767
LogS:	-4.498
# Rotatable Bonds:	4
TPSA:	128.84
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.49
Synthetic Accessibility Score:	4.069
Fsp3:	0.391
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:	-5.618
MDCK Permeability:	5.754832272941712e-06
Pgp-inhibitor:	0.012
Pgp-substrate:	0.93
Human Intestinal Absorption (HIA):	0.24
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.577

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.115
Plasma Protein Binding (PPB):	68.00505065917969%
Volume Distribution (VD):	1.01
Pgp-substrate:	7.501348972320557%

ADMET: Metabolism

CYP1A2-inhibitor:	0.212
CYP1A2-substrate:	0.258
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.211
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.652
CYP2D6-inhibitor:	0.531
CYP2D6-substrate:	0.736
CYP3A4-inhibitor:	0.25
CYP3A4-substrate:	0.084

ADMET: Excretion

Clearance (CL):	7.305
Half-life (T1/2):	0.688

ADMET: Toxicity

hERG Blockers:	0.208
Human Hepatotoxicity (H-HT):	0.148
Drug-inuced Liver Injury (DILI):	0.287
AMES Toxicity:	0.727
Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.714
Skin Sensitization:	0.936
Carcinogencity:	0.123
Eye Corrosion:	0.003
Eye Irritation:	0.032
Respiratory Toxicity:	0.399

Download Data

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

Natural Product: NPC83341

Natural Product ID:	NPC83341
*Common Name:**	FTFOYHIOGXYMQF-XIAJQQPNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FTFOYHIOGXYMQF-XIAJQQPNSA-N
Standard InCHI:	InChI=1S/C23H26O8/c1-11-20(26)21(27)22(28)23(30-11)31-19-9-17-15-6-5-14(25)7-12(15)3-4-13(10-24)16(17)8-18(19)29-2/h4-9,11,20-28H,3,10H2,1-2H3/t11-,20-,21+,22+,23-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1cc2-c3ccc(cc3CC=C(CO)c2cc1OC)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102345053
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO9305	Iotrochota purpurea	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10924179]
NPO8035	Tylophora tanakae	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350151]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	stems	Wulai Hsiang, Taipei County, Taiwan	2005-MAY	PMID[17253858]
NPO2298	Streptomyces platensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19581087]
NPO2298	Streptomyces platensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20299229]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	bark	n.a.	n.a.	PMID[20363129]
NPO2298	Streptomyces platensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21214253]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23025417]
NPO9305	Iotrochota purpurea	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	PMID[23131412]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	stem bark	Laifeng, Hubei Province, China	2012-JUL	PMID[26087384]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	Fruit juice	n.a.	n.a.	PMID[3404148]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12436	Quercus imbricaria	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12308	Metridium senile	Species	Metridiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11699	Ecballium elaterium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12669	Cassine papillosa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6253	Conus pulicarius	Species	Conidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4138	Betula platyphylla	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2298	Streptomyces platensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5384	Ligustrum obtusifolium	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12544	Dioscorea olfersiana	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20291	Phyllanthus oligospermus	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11256	Pseudowintera colorata	Species	Winteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9305	Iotrochota purpurea	Species	Iotrochotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10737	Asteriscus aquaticus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5823	Helichrysum auriceps	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9922	Myelobia smerintha	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11553	Phebalium dentatum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3736	Scrophularia koelzii	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7709	Spiracantha cornifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12188	Datisca glomerata	Species	Datiscaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9672	Lotus ucrainicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7045	Viviparus japonicus	Species	Viviparidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8035	Tylophora tanakae	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2608	Solanum andigena	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9509	Charpentiera obovata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10393	Ophidiaster ophidianus	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5008	Hubertia tomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15252	Clathria prolifera	Species	Microcionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4493	Polygonum flaccidum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8477	Myristica cagayanensis	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3378	Alstonia undulifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11811	Capparis ovata	Species	Capparaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO761	Fagus fusca	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12888	Echinus microtuberculatus	Species	Echinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1182	Croton montevidensis	Species	Euphorbiaceae	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 NPC83341 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	410
0.1-0.2	1494
0.2-0.3	3722
0.3-0.4	9780
0.4-0.5	8805
0.5-0.6	4640
0.6-0.7	8314
0.7-0.8	4273
0.8-0.85	926
0.85-0.9	252
0.9-0.95	76
0.95-1	5

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 NPC83341 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	334
0.1-0.2	843
0.2-0.3	1734
0.3-0.4	2735
0.4-0.5	1782
0.5-0.6	955
0.6-0.7	628
0.7-0.8	132
0.8-0.85	6
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