NPASS Compound

Structure

NPC55407 OpenBabel06302215172D 30 33 0 0 1 0 0 0 0 0999 V2000 0.8660 2.5000 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 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 -0.8660 2.5000 0.0000 C 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 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 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 O 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 -0.8660 -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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -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 O 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 -5.1962 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 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 -5.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 30 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 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 17 1 6 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 1 0 0 0 20 21 1 0 0 0 0 20 27 1 6 0 0 0 21 22 1 0 0 0 0 21 26 1 1 0 0 0 22 23 1 6 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	422.08
Volume:	381.192
LogP:	-0.099
LogD:	-0.199
LogS:	-3.316
# Rotatable Bonds:	3
TPSA:	190.28
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.207
Synthetic Accessibility Score:	4.036
Fsp3:	0.316
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.301
MDCK Permeability:	1.0612737241899595e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.816
Human Intestinal Absorption (HIA):	0.703
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.03
Plasma Protein Binding (PPB):	86.04717254638672%
Volume Distribution (VD):	0.911
Pgp-substrate:	19.135547637939453%

ADMET: Metabolism

CYP1A2-inhibitor:	0.139
CYP1A2-substrate:	0.074
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.379
CYP2D6-inhibitor:	0.066
CYP2D6-substrate:	0.176
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.009

ADMET: Excretion

Clearance (CL):	2.293
Half-life (T1/2):	0.904

ADMET: Toxicity

hERG Blockers:	0.1
Human Hepatotoxicity (H-HT):	0.051
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.772
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.9
Carcinogencity:	0.06
Eye Corrosion:	0.004
Eye Irritation:	0.43
Respiratory Toxicity:	0.027

Download Data

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

Natural Product: NPC55407

Natural Product ID:	NPC55407
*Common Name:**	VPQXRORFMPZBTB-IEXOMYFASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VPQXRORFMPZBTB-IEXOMYFASA-N
Standard InCHI:	InChI=1S/C19H18O11/c20-5-11-15(24)17(26)18(27)19(30-11)29-10-4-6(21)3-9-12(10)16(25)13-8(28-9)2-1-7(22)14(13)23/h1-4,11,15,17-24,26-27H,5H2/t11-,15-,17+,18-,19-/m1/s1
SMILES:	c1cc2c(c(c1O)O)c(=O)c1c(cc(cc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)o2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5321888
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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
NPO28094	Consolida oliveriana	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19489596]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23265441]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561894]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7908950]
NPO28586	Pyrus calleryana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8844	Stillingia sylvatica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28457	Siler trilobum	Species	Salticidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19861	Drypetes molunduana	Species	Putranjivaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28457	Siler trilobum	Species	Salticidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28586	Pyrus calleryana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28149	Polygala fallax	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8844	Stillingia sylvatica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28852	Euphorbia makinoi	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28586	Pyrus calleryana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28417	Monnina emarginata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8844	Stillingia sylvatica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28366	Cladonia furcata	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23442	Cachonina hallii	Species	Heterocapsaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14940	Cedronella cana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15801	Hunteria umbellata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28252	Lophozia barbata	Species	Scapaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28852	Euphorbia makinoi	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28586	Pyrus calleryana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19861	Drypetes molunduana	Species	Putranjivaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28094	Consolida oliveriana	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7994	Derris laxiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16479	Tigridia pavonia	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28793	Wettsteinia inversa	Species	Adelanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28457	Siler trilobum	Species	Salticidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20937	Heterocapsa niei	Species	Heterocapsaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28532	Streptomyces gougerotii	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28020	Hypaphorus subumbrans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO27923	Calophyllum apetalum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28149	Polygala fallax	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13329	Tephrosia polystachyoides	Species	Geometridae	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 NPC55407 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	456
0.1-0.2	1864
0.2-0.3	4318
0.3-0.4	10001
0.4-0.5	8083
0.5-0.6	4102
0.6-0.7	5219
0.7-0.8	5201
0.8-0.85	1669
0.85-0.9	1252
0.9-0.95	390
0.95-1	142

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 NPC55407 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	418
0.1-0.2	951
0.2-0.3	1964
0.3-0.4	2705
0.4-0.5	1758
0.5-0.6	902
0.6-0.7	281
0.7-0.8	130
0.8-0.85	17
0.85-0.9	15
0.9-0.95	8
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