NPASS Compound

Structure

NPC245789 OpenBabel06302215432D 38 41 0 0 1 0 0 0 0 0999 V2000 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 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 1.0000 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 2.5981 -0.5000 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 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 C 0 0 0 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 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 4.3301 -0.5000 0.0000 O 0 3 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 2.5981 -3.5000 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 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 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 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 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 -6.0622 -0.5000 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 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 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 38 1 0 0 0 0 4 5 2 0 0 0 0 4 37 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 16 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 19 1 0 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 18 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 17 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 33 1 0 0 0 0 21 22 1 0 0 0 0 21 36 1 6 0 0 0 22 23 1 0 0 0 0 22 35 1 1 0 0 0 23 24 1 0 0 0 0 23 34 1 6 0 0 0 24 25 1 1 0 0 0 24 33 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 M CHG 1 16 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	535.11
Volume:	487.451
LogP:	0.783
LogD:	0.156
LogS:	-3.59
# Rotatable Bonds:	8
TPSA:	234.97
# H-Bond Aceptor:	14
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.089
Synthetic Accessibility Score:	4.407
Fsp3:	0.292
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.606
MDCK Permeability:	7.124839612515643e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.905
Human Intestinal Absorption (HIA):	0.555
20% Bioavailability (F20%):	0.053
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025
Plasma Protein Binding (PPB):	86.7787094116211%
Volume Distribution (VD):	0.617
Pgp-substrate:	14.879473686218262%

ADMET: Metabolism

CYP1A2-inhibitor:	0.154
CYP1A2-substrate:	0.023
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.041
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.193
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.132
CYP3A4-inhibitor:	0.027
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	7.188
Half-life (T1/2):	0.965

ADMET: Toxicity

hERG Blockers:	0.145
Human Hepatotoxicity (H-HT):	0.157
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.769
Rat Oral Acute Toxicity:	0.033
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.869
Carcinogencity:	0.155
Eye Corrosion:	0.003
Eye Irritation:	0.851
Respiratory Toxicity:	0.036

Download Data

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

Natural Product: NPC245789

Natural Product ID:	NPC245789
*Common Name:**	ROQLTZUOXIQBDO-JZWLZXDTSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ROQLTZUOXIQBDO-JZWLZXDTSA-O
Standard InCHI:	InChI=1S/C24H22O14/c25-10-4-13(27)11-6-16(23(36-15(11)5-10)9-1-2-12(26)14(28)3-9)37-24-22(34)21(33)20(32)17(38-24)8-35-19(31)7-18(29)30/h1-6,17,20-22,24,32-34H,7-8H2,(H4-,25,26,27,28,29,30)/p+1/t17-,20-,21+,22-,24-/m1/s1
SMILES:	c1cc(c(cc1c1c(cc2c(cc(cc2[o+]1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)CC(=O)O)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	443915
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0001361] Anthocyanins [CHEMONTID:0002996] Anthocyanidin-3-O-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
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.1016/j.foodchem.2009.03.042]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.3136/fstr.15.499]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB10.140]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	DOI[10.5897/AJB2010.000-3252]
NPO22093	Miliusa sinensis	Species	Annonaceae	Eukaryota	dried leaves, twigs, and flowers	Vietnam	n.a.	PMID[16420055]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[17238120]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17432574]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[18405608]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[18661821]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21417376]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21627108]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	Tongxiang, China	n.a.	PMID[24621197]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	Flowers	n.a.	n.a.	PMID[28248102]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[7700984]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO2143	Rubus adenotrichos	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1854	Cardiospermum hirsutum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1854	Cardiospermum hirsutum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10756	Callitris drummondii	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO978	Panzerina lanata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10017	Echium pininana	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22273	Angelica pubescens	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2143	Rubus adenotrichos	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1854	Cardiospermum hirsutum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22093	Miliusa sinensis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4728	Streptomyces tsukubensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8002	Solanum olgae	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20306	Cheiropteris palmatopedata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20440	Chrysanthemum x morifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO127	Phragmites australis	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6604	Melanothamnus afaqhusainii	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5641	Dendroctonus frontalis	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22537	Anthelia juratzkana	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1899	Aria rostellata	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2832	Hazunta membranacea	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4706	Streptomyces vinaceusdrappus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4787	Capuronianthus mahafalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19841	Potamilla occelata	Species	Sabellidae	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 NPC245789 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	1776
0.2-0.3	4163
0.3-0.4	9305
0.4-0.5	8596
0.5-0.6	4438
0.6-0.7	5215
0.7-0.8	5384
0.8-0.85	1774
0.85-0.9	993
0.9-0.95	434
0.95-1	189

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 NPC245789 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	382
0.1-0.2	952
0.2-0.3	2004
0.3-0.4	2607
0.4-0.5	1832
0.5-0.6	887
0.6-0.7	314
0.7-0.8	125
0.8-0.85	21
0.85-0.9	17
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