NPASS Compound

Structure

NPC53802 OpenBabel06302215162D 29 31 0 0 1 0 0 0 0 0999 V2000 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 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 -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 -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 1 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 2.0000 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 0.8660 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 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 3.4641 0.0000 0.0000 C 0 0 1 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 2 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 1 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 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 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 0.0000 -0.0000 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 -0.0000 3.0000 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 1 2 2 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 6 7 2 0 0 0 0 6 9 1 0 0 0 0 7 8 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 26 1 0 0 0 0 11 12 1 0 0 0 0 11 29 1 6 0 0 0 12 13 1 0 0 0 0 12 28 1 1 0 0 0 13 14 1 0 0 0 0 13 27 1 6 0 0 0 14 15 1 1 0 0 0 14 26 1 0 0 0 0 15 16 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 18 25 1 6 0 0 0 19 20 1 0 0 0 0 19 24 1 1 0 0 0 20 21 1 0 0 0 0 20 23 1 6 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	414.15
Volume:	388.867
LogP:	-0.287
LogD:	-0.395
LogS:	-2.156
# Rotatable Bonds:	6
TPSA:	158.3
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.307
Synthetic Accessibility Score:	4.287
Fsp3:	0.579
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:	-5.73
MDCK Permeability:	2.4534283511457033e-05
Pgp-inhibitor:	0.012
Pgp-substrate:	0.976
Human Intestinal Absorption (HIA):	0.889
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.152
Plasma Protein Binding (PPB):	66.59069061279297%
Volume Distribution (VD):	0.585
Pgp-substrate:	32.88272476196289%

ADMET: Metabolism

CYP1A2-inhibitor:	0.048
CYP1A2-substrate:	0.027
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.215
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.068
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.215
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.016

ADMET: Excretion

Clearance (CL):	0.967
Half-life (T1/2):	0.627

ADMET: Toxicity

hERG Blockers:	0.467
Human Hepatotoxicity (H-HT):	0.057
Drug-inuced Liver Injury (DILI):	0.137
AMES Toxicity:	0.386
Rat Oral Acute Toxicity:	0.338
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.917
Carcinogencity:	0.54
Eye Corrosion:	0.005
Eye Irritation:	0.372
Respiratory Toxicity:	0.045

Download Data

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

Natural Product: NPC53802

Natural Product ID:	NPC53802
*Common Name:**	DZMYOBBWRZTUTA-BMVMOQKNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DZMYOBBWRZTUTA-BMVMOQKNSA-N
Standard InCHI:	InChI=1S/C19H26O10/c1-2-9-3-5-10(6-4-9)28-19-17(25)15(23)14(22)12(29-19)8-27-18-16(24)13(21)11(20)7-26-18/h2-6,11-25H,1,7-8H2/t11-,12-,13+,14-,15+,16-,17-,18+,19-/m1/s1
SMILES:	C=Cc1ccc(cc1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	185053
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
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1039/C39770000295]
NPO7574	Garcinia pyrifera	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10978200]
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11429258]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	stem bark	Medicinal Plant Garden, College of Pharmacy, Ewha Womans University	2013-DEC	PMID[28787158]
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	stem	n.a.	PMID[8945767]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9599262]
NPO11785	Citrus hassaku	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8681	Artemisia lactiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13087	Pteridium aquilinum	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2551	Plumbagella micrantha	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2551	Plumbagella micrantha	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13087	Pteridium aquilinum	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8681	Artemisia lactiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11785	Citrus hassaku	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10861	Dipsacus asper	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2551	Plumbagella micrantha	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12516	Phalaris canariensis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8389	Ophryosporus floribundus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12858	Jacaranda chelonia	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO716	Greenwayodendron oliveri	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7574	Garcinia pyrifera	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12971	Payena lucida	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13121	Crepidiastrum sonchifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11531	Duguetia calycina	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5727	Hymenothrix wislizenii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7313	Epirrhoe sperryi	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12411	Eriostemon spicatus	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1776	Attalea excelsa	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8681	Artemisia lactiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9835	Catalpa ovata	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13087	Pteridium aquilinum	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12030	Streptomyces yokosukanensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29535	Samadera indica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27659	Tanacetum parthenifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10861	Dipsacus asper	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11214	Rivina humilis	Species	Petiveriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11032	Coutarea latifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11785	Citrus hassaku	Species	Rutaceae	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 NPC53802 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	357
0.1-0.2	1495
0.2-0.3	4239
0.3-0.4	10935
0.4-0.5	7716
0.5-0.6	7452
0.6-0.7	7992
0.7-0.8	2134
0.8-0.85	250
0.85-0.9	113
0.9-0.95	14
0.95-1	0

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 NPC53802 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	287
0.1-0.2	814
0.2-0.3	1761
0.3-0.4	2881
0.4-0.5	1800
0.5-0.6	1040
0.6-0.7	512
0.7-0.8	53
0.8-0.85	1
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