NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	254.06
Volume:	256.396
LogP:	3.58
LogD:	2.571
LogS:	-4.067
# Rotatable Bonds:	0
TPSA:	74.6
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.644
Synthetic Accessibility Score:	2.164
Fsp3:	0.067
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.975
MDCK Permeability:	1.4679728337796405e-05
Pgp-inhibitor:	0.156
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.148
Plasma Protein Binding (PPB):	100.14124298095703%
Volume Distribution (VD):	0.437
Pgp-substrate:	0.7530691623687744%

ADMET: Metabolism

CYP1A2-inhibitor:	0.94
CYP1A2-substrate:	0.29
CYP2C19-inhibitor:	0.231
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.625
CYP2C9-substrate:	0.294
CYP2D6-inhibitor:	0.405
CYP2D6-substrate:	0.187
CYP3A4-inhibitor:	0.472
CYP3A4-substrate:	0.157

ADMET: Excretion

Clearance (CL):	6.692
Half-life (T1/2):	0.182

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.054
Drug-inuced Liver Injury (DILI):	0.919
AMES Toxicity:	0.88
Rat Oral Acute Toxicity:	0.203
Maximum Recommended Daily Dose:	0.773
Skin Sensitization:	0.289
Carcinogencity:	0.881
Eye Corrosion:	0.004
Eye Irritation:	0.96
Respiratory Toxicity:	0.055

Download Data

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

Natural Product: NPC53206

Natural Product ID:	NPC53206
*Common Name:**	Rubiadin
IUPAC Name:	1,3-dihydroxy-2-methylanthracene-9,10-dione
Synonyms:
Standard InCHIKey:	IRZTUXPRIUZXMP-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C15H10O4/c1-7-11(16)6-10-12(13(7)17)15(19)9-5-3-2-4-8(9)14(10)18/h2-6,16-17H,1H3
SMILES:	Cc1c(cc2c(c1O)C(=O)c1ccccc1C2=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL251251
PubChem CID:	124062
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11348221]
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520235]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350148]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1254564]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762798]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[15844957]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[16378361]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruits	Tahiti	n.a.	PMID[17378609]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[17480098]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	roots	n.a.	n.a.	PMID[18076142]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18078747]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18855442]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20192236]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21044847]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	roots	n.a.	n.a.	PMID[21973054]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	root	n.a.	PMID[21973054]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22860454]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24224843]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25590529]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26195800]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27196335]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[32083868]
NPO20880	Conocybe siliginea	Species	Bolbitiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32816486]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8626242]
NPO23980	Rhamnus nakaharai	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691213]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8882438]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30535	Morinda umbellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6050	Hymenodictyon excelsum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21199	Alangium platanifolium	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31187	Rabdosia rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3011	Rubia wallichiana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO20572	Vepris louisii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2784	Radix rubiae	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6050	Hymenodictyon excelsum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3011	Rubia wallichiana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4192	Gynochthodes umbellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21199	Alangium platanifolium	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30972	Morinda officinalis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31187	Rabdosia rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6050	Hymenodictyon excelsum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30535	Morinda umbellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16765	Knoxia valerianoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28626	Isodon rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20880	Conocybe siliginea	Species	Bolbitiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20064	Litsea konishii	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20364	Ophelia bicornis	Species	Opheliidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15980	Croton penduliflorus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3011	Rubia wallichiana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11305	Garcinia cantleyana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19792	Populus tomentosa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3376	Eriostemon brucei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11827	Zerynthia polyxena	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7106	Talaromyces helicus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6050	Hymenodictyon excelsum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26368	Fomes tasmanicus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20822	Asperula odora	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19956	Pulveroboletus retipes	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18675	Pteris aquilina	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24656	Scabiosa olgae	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10807	Melanothamnus somalensis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4192	Gynochthodes umbellata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20572	Vepris louisii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8020	Lychnophora columnaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23980	Rhamnus nakaharai	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10967	Parmelia gigas	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6430	Cercosporina kikuchii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21199	Alangium platanifolium	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13014	Ipomoea cairica	Species	Convolvulaceae	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

Activity Type	# Activity
IC50	6
Others	2

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT90	Cell Line	DU-145	Homo sapiens	IC50	=	32000.0	nM	PMID[499339]
NPT2844	Cell Line	MES-SA	Homo sapiens	IC50	=	38000.0	nM	PMID[499339]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	56000.0	nM	PMID[499339]
NPT2	Others	Unspecified		Activity	=	8.1	uM	PMID[499338]
NPT27	Others	Unspecified		IC50	>	74000.0	nM	PMID[499338]
NPT2	Others	Unspecified		Ratio	>	9.0	n.a.	PMID[499338]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	42000.0	nM	PMID[499339]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	35000.0	nM	PMID[499339]

☑ 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 NPC53206 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	424
0.1-0.2	1788
0.2-0.3	4144
0.3-0.4	11131
0.4-0.5	7575
0.5-0.6	5092
0.6-0.7	6105
0.7-0.8	5242
0.8-0.85	819
0.85-0.9	285
0.9-0.95	70
0.95-1	22

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC53414
0.9923	High Similarity	NPC254847
0.9848	High Similarity	NPC138099
0.9848	High Similarity	NPC242994
0.9847	High Similarity	NPC471905
0.9774	High Similarity	NPC181560
0.9774	High Similarity	NPC169452
0.9769	High Similarity	NPC44437
0.9699	High Similarity	NPC143438
0.9692	High Similarity	NPC267205
0.963	High Similarity	NPC193555
0.9556	High Similarity	NPC246638
0.9556	High Similarity	NPC204045
0.9556	High Similarity	NPC305845
0.9552	High Similarity	NPC190457
0.9489	High Similarity	NPC193703
0.9489	High Similarity	NPC21599
0.9485	High Similarity	NPC73061
0.9485	High Similarity	NPC135524
0.9474	High Similarity	NPC191976
0.947	High Similarity	NPC282780
0.947	High Similarity	NPC166480
0.9412	High Similarity	NPC290550
0.9385	High Similarity	NPC99731
0.9348	High Similarity	NPC244691
0.9348	High Similarity	NPC471906
0.9348	High Similarity	NPC48762
0.9338	High Similarity	NPC203063
0.9308	High Similarity	NPC282923
0.9281	High Similarity	NPC34482
0.9254	High Similarity	NPC161632
0.9214	High Similarity	NPC470570
0.9203	High Similarity	NPC474961
0.9191	High Similarity	NPC4214
0.9191	High Similarity	NPC13715
0.9191	High Similarity	NPC61398
0.9191	High Similarity	NPC416
0.9185	High Similarity	NPC118919
0.9154	High Similarity	NPC8745
0.9149	High Similarity	NPC118027
0.9149	High Similarity	NPC245584
0.9149	High Similarity	NPC37709
0.9149	High Similarity	NPC289042
0.9149	High Similarity	NPC190648
0.9149	High Similarity	NPC126767
0.9149	High Similarity	NPC56433
0.9149	High Similarity	NPC312929
0.9137	High Similarity	NPC474203
0.9137	High Similarity	NPC295712
0.9137	High Similarity	NPC451542
0.9137	High Similarity	NPC313047
0.9137	High Similarity	NPC238629
0.9111	High Similarity	NPC283088
0.9104	High Similarity	NPC52407
0.9098	High Similarity	NPC205992
0.9098	High Similarity	NPC93015
0.9091	High Similarity	NPC92624
0.9091	High Similarity	NPC255641
0.9091	High Similarity	NPC290954
0.9077	High Similarity	NPC10926
0.9077	High Similarity	NPC103540
0.9071	High Similarity	NPC19896
0.9037	High Similarity	NPC50924
0.903	High Similarity	NPC175738
0.903	High Similarity	NPC70622
0.9023	High Similarity	NPC259942
0.9023	High Similarity	NPC31799
0.9008	High Similarity	NPC160499
0.9	High Similarity	NPC142956
0.9	High Similarity	NPC13238
0.9	High Similarity	NPC173978
0.9	High Similarity	NPC293545
0.9	High Similarity	NPC174905
0.8993	High Similarity	NPC187843
0.8993	High Similarity	NPC110810
0.8978	High Similarity	NPC53001
0.8971	High Similarity	NPC258502
0.8971	High Similarity	NPC80035
0.8963	High Similarity	NPC48036
0.8963	High Similarity	NPC225051
0.8963	High Similarity	NPC115458
0.8958	High Similarity	NPC294646
0.8958	High Similarity	NPC470568
0.8958	High Similarity	NPC147735
0.8951	High Similarity	NPC471907
0.8947	High Similarity	NPC109123
0.8947	High Similarity	NPC474998
0.8944	High Similarity	NPC110882
0.8944	High Similarity	NPC85393
0.8944	High Similarity	NPC271944
0.8939	High Similarity	NPC100067
0.8939	High Similarity	NPC266689
0.8939	High Similarity	NPC169250
0.8939	High Similarity	NPC98254
0.8939	High Similarity	NPC190043
0.8939	High Similarity	NPC105157
0.8939	High Similarity	NPC162612
0.8939	High Similarity	NPC30501
0.8939	High Similarity	NPC72158
0.8939	High Similarity	NPC103356
0.8939	High Similarity	NPC23126
0.8936	High Similarity	NPC10764
0.8936	High Similarity	NPC227841
0.8929	High Similarity	NPC239136
0.8929	High Similarity	NPC19631
0.8923	High Similarity	NPC375356
0.8921	High Similarity	NPC183345
0.8913	High Similarity	NPC87723
0.8904	High Similarity	NPC208806
0.8897	High Similarity	NPC12070
0.8897	High Similarity	NPC474519
0.8897	High Similarity	NPC288089
0.8897	High Similarity	NPC470569
0.8881	High Similarity	NPC62219
0.8881	High Similarity	NPC136588
0.8881	High Similarity	NPC199253
0.8873	High Similarity	NPC12402
0.8872	High Similarity	NPC473017
0.8872	High Similarity	NPC221777
0.8872	High Similarity	NPC48248
0.8872	High Similarity	NPC21305
0.8872	High Similarity	NPC179898
0.8865	High Similarity	NPC66593
0.8865	High Similarity	NPC296752
0.8865	High Similarity	NPC471682
0.8864	High Similarity	NPC62952
0.8864	High Similarity	NPC3224
0.8864	High Similarity	NPC267846
0.8849	High Similarity	NPC26924
0.8849	High Similarity	NPC162939
0.8846	High Similarity	NPC91478
0.8846	High Similarity	NPC32032
0.8846	High Similarity	NPC133909
0.8846	High Similarity	NPC300274
0.8844	High Similarity	NPC66508
0.8844	High Similarity	NPC226656
0.8841	High Similarity	NPC290030
0.8836	High Similarity	NPC40356
0.8836	High Similarity	NPC154683
0.8832	High Similarity	NPC249272
0.8832	High Similarity	NPC290803
0.8828	High Similarity	NPC280295
0.8828	High Similarity	NPC205766
0.8824	High Similarity	NPC314048
0.8824	High Similarity	NPC180261
0.8824	High Similarity	NPC114183
0.8824	High Similarity	NPC53896
0.8824	High Similarity	NPC294226
0.8824	High Similarity	NPC37299
0.8815	High Similarity	NPC72669
0.8815	High Similarity	NPC244699
0.8815	High Similarity	NPC474517
0.8806	High Similarity	NPC146647
0.8806	High Similarity	NPC34414
0.8797	High Similarity	NPC116513
0.8794	High Similarity	NPC94076
0.8794	High Similarity	NPC182255
0.8794	High Similarity	NPC137649
0.8794	High Similarity	NPC257644
0.8788	High Similarity	NPC477454
0.8786	High Similarity	NPC156872
0.8786	High Similarity	NPC315578
0.8784	High Similarity	NPC470564
0.8776	High Similarity	NPC214632
0.8776	High Similarity	NPC107109
0.8769	High Similarity	NPC19174
0.8769	High Similarity	NPC73532
0.8769	High Similarity	NPC115159
0.8769	High Similarity	NPC45438
0.8769	High Similarity	NPC224273
0.8769	High Similarity	NPC242895
0.8769	High Similarity	NPC143427
0.8769	High Similarity	NPC267552
0.8769	High Similarity	NPC120545
0.8769	High Similarity	NPC156139
0.8768	High Similarity	NPC474813
0.8768	High Similarity	NPC194764
0.8768	High Similarity	NPC65005
0.8768	High Similarity	NPC264112
0.8768	High Similarity	NPC315275
0.8768	High Similarity	NPC272268
0.8768	High Similarity	NPC155211
0.8767	High Similarity	NPC35
0.8759	High Similarity	NPC329933
0.8759	High Similarity	NPC270899
0.875	High Similarity	NPC135801
0.875	High Similarity	NPC58685
0.875	High Similarity	NPC290194
0.875	High Similarity	NPC34802
0.8741	High Similarity	NPC147757
0.8741	High Similarity	NPC471683
0.8741	High Similarity	NPC49282
0.8732	High Similarity	NPC167663
0.8732	High Similarity	NPC84266
0.8725	High Similarity	NPC178976
0.8722	High Similarity	NPC231774
0.8722	High Similarity	NPC473691
0.8722	High Similarity	NPC96915
0.8714	High Similarity	NPC472903
0.8707	High Similarity	NPC312338

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 NPC53206 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	402
0.1-0.2	970
0.2-0.3	1493
0.3-0.4	2892
0.4-0.5	1972
0.5-0.6	984
0.6-0.7	315
0.7-0.8	108
0.8-0.85	8
0.85-0.9	4
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9923	High Similarity	NPD1509	Clinical (unspecified phase)
0.9077	High Similarity	NPD1470	Approved
0.8936	High Similarity	NPD7390	Discontinued
0.8769	High Similarity	NPD1201	Approved
0.875	High Similarity	NPD943	Approved
0.8571	High Similarity	NPD5406	Approved
0.8571	High Similarity	NPD5408	Approved
0.8571	High Similarity	NPD5405	Approved
0.8571	High Similarity	NPD5404	Approved
0.8369	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.8357	Intermediate Similarity	NPD1607	Approved
0.8258	Intermediate Similarity	NPD6232	Discontinued
0.8239	Intermediate Similarity	NPD1510	Phase 2
0.8217	Intermediate Similarity	NPD7473	Discontinued
0.8214	Intermediate Similarity	NPD1240	Approved
0.8168	Intermediate Similarity	NPD405	Clinical (unspecified phase)
0.8039	Intermediate Similarity	NPD7819	Suspended
0.8013	Intermediate Similarity	NPD3226	Approved
0.7987	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7987	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.7971	Intermediate Similarity	NPD1164	Approved
0.7962	Intermediate Similarity	NPD6959	Discontinued
0.7945	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7945	Intermediate Similarity	NPD1549	Phase 2
0.7877	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7877	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7867	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.7867	Intermediate Similarity	NPD2532	Approved
0.7867	Intermediate Similarity	NPD2534	Approved
0.7867	Intermediate Similarity	NPD2533	Approved
0.7806	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.78	Intermediate Similarity	NPD1511	Approved
0.7771	Intermediate Similarity	NPD3749	Approved
0.7756	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7755	Intermediate Similarity	NPD2346	Discontinued
0.7727	Intermediate Similarity	NPD4380	Phase 2
0.7718	Intermediate Similarity	NPD3750	Approved
0.7697	Intermediate Similarity	NPD1512	Approved
0.7687	Intermediate Similarity	NPD2935	Discontinued
0.7677	Intermediate Similarity	NPD7411	Suspended
0.7628	Intermediate Similarity	NPD1934	Approved
0.758	Intermediate Similarity	NPD2801	Approved
0.7569	Intermediate Similarity	NPD3764	Approved
0.7568	Intermediate Similarity	NPD2796	Approved
0.7547	Intermediate Similarity	NPD7075	Discontinued
0.7536	Intermediate Similarity	NPD3019	Approved
0.7533	Intermediate Similarity	NPD2800	Approved
0.7517	Intermediate Similarity	NPD2344	Approved
0.75	Intermediate Similarity	NPD9269	Phase 2
0.7485	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.7484	Intermediate Similarity	NPD7768	Phase 2
0.7484	Intermediate Similarity	NPD3882	Suspended
0.7468	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7464	Intermediate Similarity	NPD4196	Clinical (unspecified phase)
0.7464	Intermediate Similarity	NPD9268	Approved
0.7455	Intermediate Similarity	NPD6020	Phase 2
0.7455	Intermediate Similarity	NPD5844	Phase 1
0.745	Intermediate Similarity	NPD1551	Phase 2
0.741	Intermediate Similarity	NPD2932	Approved
0.7389	Intermediate Similarity	NPD6599	Discontinued
0.7386	Intermediate Similarity	NPD3300	Phase 2
0.7383	Intermediate Similarity	NPD3299	Clinical (unspecified phase)
0.7383	Intermediate Similarity	NPD2799	Discontinued
0.7383	Intermediate Similarity	NPD3748	Approved
0.7368	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7346	Intermediate Similarity	NPD5494	Approved
0.7341	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD6100	Approved
0.7333	Intermediate Similarity	NPD6099	Approved
0.732	Intermediate Similarity	NPD2309	Approved
0.7303	Intermediate Similarity	NPD1243	Approved
0.7303	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7297	Intermediate Similarity	NPD230	Phase 1
0.7296	Intermediate Similarity	NPD6801	Discontinued
0.7293	Intermediate Similarity	NPD9266	Approved
0.7293	Intermediate Similarity	NPD74	Approved
0.7285	Intermediate Similarity	NPD1471	Phase 3
0.7273	Intermediate Similarity	NPD6166	Phase 2
0.7273	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7256	Intermediate Similarity	NPD5711	Approved
0.7256	Intermediate Similarity	NPD5710	Approved
0.7255	Intermediate Similarity	NPD7003	Approved
0.725	Intermediate Similarity	NPD1465	Phase 2
0.7248	Intermediate Similarity	NPD6651	Approved
0.7246	Intermediate Similarity	NPD9493	Approved
0.7239	Intermediate Similarity	NPD4750	Phase 3
0.7226	Intermediate Similarity	NPD6799	Approved
0.7226	Intermediate Similarity	NPD5951	Approved
0.7222	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD6559	Discontinued
0.7218	Intermediate Similarity	NPD9264	Approved
0.7218	Intermediate Similarity	NPD9265	Clinical (unspecified phase)
0.7218	Intermediate Similarity	NPD2342	Discontinued
0.7218	Intermediate Similarity	NPD9263	Approved
0.7218	Intermediate Similarity	NPD9267	Approved
0.7211	Intermediate Similarity	NPD2313	Discontinued
0.7209	Intermediate Similarity	NPD8150	Discontinued
0.7197	Intermediate Similarity	NPD920	Approved
0.7186	Intermediate Similarity	NPD3818	Discontinued
0.7172	Intermediate Similarity	NPD2798	Approved
0.716	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.716	Intermediate Similarity	NPD5953	Discontinued
0.7159	Intermediate Similarity	NPD6535	Approved
0.7159	Intermediate Similarity	NPD6534	Approved
0.7154	Intermediate Similarity	NPD1242	Phase 1
0.7153	Intermediate Similarity	NPD1283	Approved
0.7143	Intermediate Similarity	NPD4625	Phase 3
0.7143	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7113	Intermediate Similarity	NPD3023	Approved
0.7113	Intermediate Similarity	NPD3026	Approved
0.7107	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7107	Intermediate Similarity	NPD7458	Discontinued
0.7103	Intermediate Similarity	NPD1203	Approved
0.7099	Intermediate Similarity	NPD846	Approved
0.7099	Intermediate Similarity	NPD3817	Phase 2
0.7099	Intermediate Similarity	NPD940	Approved
0.7092	Intermediate Similarity	NPD3024	Approved
0.7092	Intermediate Similarity	NPD3025	Approved
0.7092	Intermediate Similarity	NPD1651	Approved
0.707	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7056	Intermediate Similarity	NPD6778	Approved
0.7056	Intermediate Similarity	NPD6779	Approved
0.7056	Intermediate Similarity	NPD6781	Approved
0.7056	Intermediate Similarity	NPD6780	Approved
0.7056	Intermediate Similarity	NPD6782	Approved
0.7056	Intermediate Similarity	NPD6776	Approved
0.7056	Intermediate Similarity	NPD6777	Approved
0.7051	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7041	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7039	Intermediate Similarity	NPD7700	Phase 2
0.7039	Intermediate Similarity	NPD7699	Phase 2
0.7029	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7021	Intermediate Similarity	NPD9545	Approved
0.7014	Intermediate Similarity	NPD3972	Approved
0.7006	Intermediate Similarity	NPD3926	Phase 2
0.7	Intermediate Similarity	NPD7074	Phase 3
0.6988	Remote Similarity	NPD1247	Approved
0.6981	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.698	Remote Similarity	NPD411	Approved
0.6978	Remote Similarity	NPD9281	Approved
0.6977	Remote Similarity	NPD4419	Clinical (unspecified phase)
0.697	Remote Similarity	NPD919	Approved
0.6961	Remote Similarity	NPD7501	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD7635	Approved
0.6944	Remote Similarity	NPD1281	Approved
0.6941	Remote Similarity	NPD7054	Approved
0.6941	Remote Similarity	NPD7286	Phase 2
0.694	Remote Similarity	NPD7698	Approved
0.694	Remote Similarity	NPD7696	Phase 3
0.694	Remote Similarity	NPD7435	Discontinued
0.694	Remote Similarity	NPD7697	Approved
0.6936	Remote Similarity	NPD8313	Approved
0.6936	Remote Similarity	NPD8312	Approved
0.6935	Remote Similarity	NPD8151	Discontinued
0.6928	Remote Similarity	NPD4308	Phase 3
0.6923	Remote Similarity	NPD4628	Phase 3
0.6923	Remote Similarity	NPD7163	Clinical (unspecified phase)
0.6918	Remote Similarity	NPD1876	Approved
0.6917	Remote Similarity	NPD9261	Approved
0.691	Remote Similarity	NPD6213	Phase 3
0.691	Remote Similarity	NPD6214	Clinical (unspecified phase)
0.691	Remote Similarity	NPD6212	Phase 3
0.6902	Remote Similarity	NPD7870	Phase 2
0.6902	Remote Similarity	NPD7871	Phase 2
0.6902	Remote Similarity	NPD8320	Phase 1
0.6902	Remote Similarity	NPD8319	Approved
0.6901	Remote Similarity	NPD7472	Approved
0.6897	Remote Similarity	NPD9717	Approved
0.689	Remote Similarity	NPD5402	Approved
0.689	Remote Similarity	NPD8438	Clinical (unspecified phase)
0.6882	Remote Similarity	NPD3751	Discontinued
0.6871	Remote Similarity	NPD37	Approved
0.6867	Remote Similarity	NPD6859	Clinical (unspecified phase)
0.6867	Remote Similarity	NPD4907	Clinical (unspecified phase)
0.686	Remote Similarity	NPD6797	Phase 2
0.6845	Remote Similarity	NPD7229	Phase 3
0.6842	Remote Similarity	NPD447	Suspended
0.6836	Remote Similarity	NPD4287	Approved
0.6828	Remote Similarity	NPD6973	Clinical (unspecified phase)
0.6828	Remote Similarity	NPD1547	Clinical (unspecified phase)
0.6821	Remote Similarity	NPD6663	Approved
0.6821	Remote Similarity	NPD7251	Discontinued
0.6815	Remote Similarity	NPD8166	Discontinued
0.6806	Remote Similarity	NPD4626	Approved
0.6806	Remote Similarity	NPD2286	Discontinued
0.6794	Remote Similarity	NPD288	Approved
0.6791	Remote Similarity	NPD7701	Phase 2
0.6788	Remote Similarity	NPD4288	Approved
0.6788	Remote Similarity	NPD2296	Approved
0.6784	Remote Similarity	NPD7177	Discontinued
0.6782	Remote Similarity	NPD7808	Phase 3
0.6782	Remote Similarity	NPD4338	Clinical (unspecified phase)
0.6781	Remote Similarity	NPD4878	Approved
0.6781	Remote Similarity	NPD1608	Approved
0.6779	Remote Similarity	NPD5736	Approved
0.6774	Remote Similarity	NPD7211	Clinical (unspecified phase)
0.6772	Remote Similarity	NPD6190	Approved
0.677	Remote Similarity	NPD5403	Approved
0.6766	Remote Similarity	NPD6234	Discontinued

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