NPASS Compound

Structure

CID13171 OpenBabel06191715342D 28 30 0 0 1 0 0 0 0 0999 V2000 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 2.5827 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 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8549 2.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 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 0.8660 -0.5000 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 1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 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 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8060 2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1118 2.1180 0.0000 O 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 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.4563 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 -1.7321 -0.0000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 3 2 0 0 0 0 3 17 1 0 0 0 0 4 18 1 0 0 0 0 5 8 2 0 0 0 0 5 26 1 0 0 0 0 6 17 1 0 0 0 0 6 19 1 0 0 0 0 7 2 1 1 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 14 1 0 0 0 0 9 4 1 1 0 0 0 9 11 1 0 0 0 0 9 27 1 0 0 0 0 10 15 1 0 0 0 0 10 17 1 1 0 0 0 11 12 1 0 0 0 0 11 20 1 6 0 0 0 12 13 1 0 0 0 0 12 21 1 1 0 0 0 13 16 1 0 0 0 0 13 22 1 6 0 0 0 14 23 2 0 0 0 0 14 25 1 0 0 0 0 15 26 1 0 0 0 0 15 28 1 6 0 0 0 16 27 1 0 0 0 0 16 28 1 1 0 0 0 17 24 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	404.13
Volume:	365.702
LogP:	-0.603
LogD:	-0.579
LogS:	-0.934
# Rotatable Bonds:	6
TPSA:	175.37
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	4.928
Fsp3:	0.706
Lipinski Rule-of-5:	Rejected
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:	-5.941
MDCK Permeability:	0.0001482335792388767
Pgp-inhibitor:	0.0
Pgp-substrate:	0.151
Human Intestinal Absorption (HIA):	0.138
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.212
Plasma Protein Binding (PPB):	18.666656494140625%
Volume Distribution (VD):	0.326
Pgp-substrate:	54.98667907714844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.401
CYP2C19-inhibitor:	0.012
CYP2C19-substrate:	0.09
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.024
CYP3A4-substrate:	0.082

ADMET: Excretion

Clearance (CL):	1.443
Half-life (T1/2):	0.849

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.149
Drug-inuced Liver Injury (DILI):	0.362
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.15
Carcinogencity:	0.931
Eye Corrosion:	0.003
Eye Irritation:	0.06
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC13171

Natural Product ID:	NPC13171
*Common Name:**	Gardenoside
IUPAC Name:	methyl (1S,4aS,7S,7aS)-7-hydroxy-7-(hydroxymethyl)-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4a,7a-dihydro-1H-cyclopenta[c]pyran-4-carboxylate
Synonyms:	Gardenoside
Standard InCHIKey:	XJMPAUZQVRGFRE-AYDWLWLASA-N
Standard InCHI:	InChI=1S/C17H24O11/c1-25-14(23)8-5-26-15(10-7(8)2-3-17(10,24)6-19)28-16-13(22)12(21)11(20)9(4-18)27-16/h2-3,5,7,9-13,15-16,18-22,24H,4,6H2,1H3/t7-,9-,10-,11-,12+,13-,15+,16+,17-/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@@H]3[C@H]2[C@](O)(CO)C=C3)C(=O)OC)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1079679
PubChem CID:	442423
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid 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
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10425120]
NPO8164	Haliclona vansoesti	Species	Chalinidae	Eukaryota	n.a.	caribbean	n.a.	PMID[10924178]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[16309325]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	Seoul, Korea	2000-Jun	PMID[16643034]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1667413]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[18505286]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[19650637]
NPO23142	Lamium album	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19904996]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23305920]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141747]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16259.1	Syringa reticulata subsp. amurensis	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16259.1	Syringa reticulata subsp. amurensis	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8431	Hypecoum imberbe	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17824	Genipa americana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9991	Sedum purpureum	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23142	Lamium album	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO450	Ramonda myconi	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8164	Haliclona vansoesti	Species	Chalinidae	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
Others	7

Activity Type	# Activity
Cell Line	1
Organism	2
Others	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	80.0	%	PMID[449642]
NPT2	Others	Unspecified		Inhibition	=	92.6	%	PMID[449642]
NPT2	Others	Unspecified		Inhibition	=	100.0	%	PMID[449642]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	Inhibition	=	-3.4	%	PMID[449643]
NPT191	Organism	Hepatitis C virus	Hepatitis C virus	Inhibition	=	21.1	%	PMID[449643]

☑ 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 NPC13171 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	211
0.1-0.2	1282
0.2-0.3	4438
0.3-0.4	8022
0.4-0.5	14653
0.5-0.6	9132
0.6-0.7	4389
0.7-0.8	494
0.8-0.85	46
0.85-0.9	10
0.9-0.95	15
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC195510
0.9394	High Similarity	NPC254538
0.9394	High Similarity	NPC474285
0.9375	High Similarity	NPC255677
0.9375	High Similarity	NPC22149
0.9375	High Similarity	NPC306344
0.9278	High Similarity	NPC298255
0.9278	High Similarity	NPC28304
0.9192	High Similarity	NPC86095
0.9149	High Similarity	NPC61201
0.9091	High Similarity	NPC118761
0.9091	High Similarity	NPC197541
0.9091	High Similarity	NPC234304
0.9091	High Similarity	NPC267869
0.9091	High Similarity	NPC284929
0.9062	High Similarity	NPC241911
0.899	High Similarity	NPC261117
0.899	High Similarity	NPC310804
0.899	High Similarity	NPC250545
0.899	High Similarity	NPC222062
0.8737	High Similarity	NPC117596
0.8737	High Similarity	NPC303451
0.8737	High Similarity	NPC6414
0.8646	High Similarity	NPC472125
0.8646	High Similarity	NPC472126
0.8646	High Similarity	NPC472124
0.8571	High Similarity	NPC101051
0.8571	High Similarity	NPC170204
0.8542	High Similarity	NPC65665
0.8542	High Similarity	NPC307699
0.8542	High Similarity	NPC120021
0.8542	High Similarity	NPC216826
0.8542	High Similarity	NPC231710
0.8542	High Similarity	NPC270908
0.8542	High Similarity	NPC470573
0.8384	Intermediate Similarity	NPC469543
0.8333	Intermediate Similarity	NPC20673
0.8283	Intermediate Similarity	NPC475832
0.8283	Intermediate Similarity	NPC475927
0.8252	Intermediate Similarity	NPC471599
0.8235	Intermediate Similarity	NPC244878
0.8173	Intermediate Similarity	NPC37240
0.8155	Intermediate Similarity	NPC219038
0.8137	Intermediate Similarity	NPC151093
0.8119	Intermediate Similarity	NPC161293
0.8119	Intermediate Similarity	NPC306041
0.8113	Intermediate Similarity	NPC80338
0.8113	Intermediate Similarity	NPC197813
0.8113	Intermediate Similarity	NPC148270
0.8105	Intermediate Similarity	NPC475035
0.8077	Intermediate Similarity	NPC474730
0.8077	Intermediate Similarity	NPC35185
0.8077	Intermediate Similarity	NPC4899
0.8077	Intermediate Similarity	NPC177013
0.8041	Intermediate Similarity	NPC142583
0.8041	Intermediate Similarity	NPC475037
0.8039	Intermediate Similarity	NPC472290
0.8037	Intermediate Similarity	NPC475960
0.8019	Intermediate Similarity	NPC127235
0.8019	Intermediate Similarity	NPC170432
0.8	Intermediate Similarity	NPC280390
0.8	Intermediate Similarity	NPC475928
0.8	Intermediate Similarity	NPC320552
0.7981	Intermediate Similarity	NPC4637
0.7981	Intermediate Similarity	NPC3488
0.7981	Intermediate Similarity	NPC287539
0.7981	Intermediate Similarity	NPC98859
0.798	Intermediate Similarity	NPC327253
0.7921	Intermediate Similarity	NPC71589
0.7917	Intermediate Similarity	NPC220167
0.7917	Intermediate Similarity	NPC266718
0.7917	Intermediate Similarity	NPC136699
0.7905	Intermediate Similarity	NPC106668
0.79	Intermediate Similarity	NPC9447
0.79	Intermediate Similarity	NPC477749
0.789	Intermediate Similarity	NPC193741
0.787	Intermediate Similarity	NPC110701
0.7843	Intermediate Similarity	NPC36954
0.7835	Intermediate Similarity	NPC475034
0.7835	Intermediate Similarity	NPC470124
0.783	Intermediate Similarity	NPC27687
0.7826	Intermediate Similarity	NPC470829
0.7826	Intermediate Similarity	NPC473228
0.7822	Intermediate Similarity	NPC472196
0.7822	Intermediate Similarity	NPC472195
0.7822	Intermediate Similarity	NPC238090
0.7822	Intermediate Similarity	NPC475912
0.7812	Intermediate Similarity	NPC211455
0.7812	Intermediate Similarity	NPC188717
0.7798	Intermediate Similarity	NPC315836
0.7798	Intermediate Similarity	NPC313668
0.7788	Intermediate Similarity	NPC81483
0.7788	Intermediate Similarity	NPC472015
0.7788	Intermediate Similarity	NPC473307
0.7788	Intermediate Similarity	NPC307517
0.7788	Intermediate Similarity	NPC61630
0.7788	Intermediate Similarity	NPC169468
0.7778	Intermediate Similarity	NPC137368
0.7767	Intermediate Similarity	NPC54731
0.7757	Intermediate Similarity	NPC305157
0.7757	Intermediate Similarity	NPC307846
0.7757	Intermediate Similarity	NPC474917
0.7748	Intermediate Similarity	NPC475924
0.7748	Intermediate Similarity	NPC475851
0.7745	Intermediate Similarity	NPC159698
0.7745	Intermediate Similarity	NPC256368
0.7745	Intermediate Similarity	NPC25701
0.7745	Intermediate Similarity	NPC2003
0.7739	Intermediate Similarity	NPC48692
0.7723	Intermediate Similarity	NPC472197
0.7723	Intermediate Similarity	NPC470373
0.7723	Intermediate Similarity	NPC470379
0.7719	Intermediate Similarity	NPC475309
0.7719	Intermediate Similarity	NPC13710
0.7706	Intermediate Similarity	NPC219900
0.7706	Intermediate Similarity	NPC177524
0.7706	Intermediate Similarity	NPC392
0.77	Intermediate Similarity	NPC477748
0.7692	Intermediate Similarity	NPC40812
0.7692	Intermediate Similarity	NPC153559
0.7692	Intermediate Similarity	NPC474194
0.7685	Intermediate Similarity	NPC472751
0.7685	Intermediate Similarity	NPC41681
0.7685	Intermediate Similarity	NPC472749
0.767	Intermediate Similarity	NPC291709
0.767	Intermediate Similarity	NPC241407
0.767	Intermediate Similarity	NPC14961
0.767	Intermediate Similarity	NPC270013
0.7647	Intermediate Similarity	NPC320089
0.7647	Intermediate Similarity	NPC476300
0.7642	Intermediate Similarity	NPC198992
0.7629	Intermediate Similarity	NPC44261
0.7624	Intermediate Similarity	NPC476004
0.7624	Intermediate Similarity	NPC202886
0.7624	Intermediate Similarity	NPC474761
0.7619	Intermediate Similarity	NPC124181
0.7619	Intermediate Similarity	NPC40182
0.7619	Intermediate Similarity	NPC83895
0.7619	Intermediate Similarity	NPC187761
0.7619	Intermediate Similarity	NPC255592
0.7619	Intermediate Similarity	NPC198422
0.7619	Intermediate Similarity	NPC308567
0.7619	Intermediate Similarity	NPC261377
0.7611	Intermediate Similarity	NPC181145
0.76	Intermediate Similarity	NPC473151
0.7596	Intermediate Similarity	NPC476315
0.7596	Intermediate Similarity	NPC256230
0.7593	Intermediate Similarity	NPC472748
0.7573	Intermediate Similarity	NPC474035
0.7573	Intermediate Similarity	NPC81386
0.7573	Intermediate Similarity	NPC472198
0.7573	Intermediate Similarity	NPC294293
0.757	Intermediate Similarity	NPC80144
0.757	Intermediate Similarity	NPC201191
0.7568	Intermediate Similarity	NPC83005
0.7568	Intermediate Similarity	NPC46407
0.7549	Intermediate Similarity	NPC472199
0.7549	Intermediate Similarity	NPC184463
0.7549	Intermediate Similarity	NPC473321
0.7549	Intermediate Similarity	NPC30515
0.7547	Intermediate Similarity	NPC475053
0.7547	Intermediate Similarity	NPC473146
0.7545	Intermediate Similarity	NPC473807
0.7524	Intermediate Similarity	NPC476613
0.7524	Intermediate Similarity	NPC476612
0.7523	Intermediate Similarity	NPC239961
0.7522	Intermediate Similarity	NPC75167
0.7522	Intermediate Similarity	NPC311592
0.7521	Intermediate Similarity	NPC170880
0.75	Intermediate Similarity	NPC475186
0.75	Intermediate Similarity	NPC126897
0.75	Intermediate Similarity	NPC74139
0.75	Intermediate Similarity	NPC197736
0.75	Intermediate Similarity	NPC118077
0.75	Intermediate Similarity	NPC471142
0.75	Intermediate Similarity	NPC472750
0.75	Intermediate Similarity	NPC297945
0.75	Intermediate Similarity	NPC272050
0.75	Intermediate Similarity	NPC472747
0.7478	Intermediate Similarity	NPC23046
0.7477	Intermediate Similarity	NPC473332
0.7477	Intermediate Similarity	NPC67296
0.7477	Intermediate Similarity	NPC154127
0.7477	Intermediate Similarity	NPC476611
0.7476	Intermediate Similarity	NPC212486
0.7476	Intermediate Similarity	NPC179746
0.7476	Intermediate Similarity	NPC81419
0.7475	Intermediate Similarity	NPC470658
0.7475	Intermediate Similarity	NPC21469
0.7475	Intermediate Similarity	NPC477746
0.7475	Intermediate Similarity	NPC477747
0.7459	Intermediate Similarity	NPC213634
0.7456	Intermediate Similarity	NPC472274
0.7453	Intermediate Similarity	NPC203627
0.7453	Intermediate Similarity	NPC187268
0.7453	Intermediate Similarity	NPC471144
0.7453	Intermediate Similarity	NPC90819
0.7451	Intermediate Similarity	NPC177668
0.7451	Intermediate Similarity	NPC118078
0.7451	Intermediate Similarity	NPC473448

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 NPC13171 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	1609
0.2-0.3	3807
0.3-0.4	2346
0.4-0.5	858
0.5-0.6	284
0.6-0.7	70
0.7-0.8	4
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7706	Intermediate Similarity	NPD6686	Approved
0.7521	Intermediate Similarity	NPD8513	Phase 3
0.75	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7453	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7373	Intermediate Similarity	NPD8515	Approved
0.7373	Intermediate Similarity	NPD8516	Approved
0.7373	Intermediate Similarity	NPD8517	Approved
0.7282	Intermediate Similarity	NPD46	Approved
0.7282	Intermediate Similarity	NPD6698	Approved
0.7083	Intermediate Similarity	NPD7503	Approved
0.7048	Intermediate Similarity	NPD7983	Approved
0.6992	Remote Similarity	NPD7507	Approved
0.6952	Remote Similarity	NPD7838	Discovery
0.6842	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6838	Remote Similarity	NPD6053	Discontinued
0.6829	Remote Similarity	NPD7829	Approved
0.6829	Remote Similarity	NPD7830	Approved
0.6825	Remote Similarity	NPD7319	Approved
0.681	Remote Similarity	NPD6371	Approved
0.68	Remote Similarity	NPD8074	Phase 3
0.6731	Remote Similarity	NPD4249	Approved
0.672	Remote Similarity	NPD8451	Approved
0.6696	Remote Similarity	NPD5344	Discontinued
0.6694	Remote Similarity	NPD7642	Approved
0.6667	Remote Similarity	NPD4250	Approved
0.6667	Remote Similarity	NPD8448	Approved
0.6667	Remote Similarity	NPD5778	Approved
0.6667	Remote Similarity	NPD4251	Approved
0.6667	Remote Similarity	NPD5779	Approved
0.664	Remote Similarity	NPD8342	Approved
0.664	Remote Similarity	NPD8341	Approved
0.664	Remote Similarity	NPD8340	Approved
0.664	Remote Similarity	NPD8299	Approved
0.6636	Remote Similarity	NPD7839	Suspended
0.6612	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6602	Remote Similarity	NPD6110	Phase 1
0.6602	Remote Similarity	NPD7154	Phase 3
0.6557	Remote Similarity	NPD7327	Approved
0.6557	Remote Similarity	NPD7641	Discontinued
0.6557	Remote Similarity	NPD7328	Approved
0.6552	Remote Similarity	NPD6412	Phase 2
0.6545	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6538	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6532	Remote Similarity	NPD8033	Approved
0.6532	Remote Similarity	NPD8444	Approved
0.6518	Remote Similarity	NPD4225	Approved
0.6512	Remote Similarity	NPD8390	Approved
0.6512	Remote Similarity	NPD8392	Approved
0.6512	Remote Similarity	NPD8391	Approved
0.6504	Remote Similarity	NPD7516	Approved
0.65	Remote Similarity	NPD8133	Approved
0.648	Remote Similarity	NPD8080	Discontinued
0.6476	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.6466	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.6455	Remote Similarity	NPD5282	Discontinued
0.6452	Remote Similarity	NPD8377	Approved
0.6452	Remote Similarity	NPD8294	Approved
0.64	Remote Similarity	NPD8380	Approved
0.64	Remote Similarity	NPD8379	Approved
0.64	Remote Similarity	NPD8378	Approved
0.64	Remote Similarity	NPD8296	Approved
0.64	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.64	Remote Similarity	NPD8335	Approved
0.6341	Remote Similarity	NPD7115	Discovery
0.6316	Remote Similarity	NPD6648	Approved
0.6311	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6299	Remote Similarity	NPD8328	Phase 3
0.6239	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6239	Remote Similarity	NPD6101	Approved
0.6239	Remote Similarity	NPD1695	Approved
0.6231	Remote Similarity	NPD7736	Approved
0.622	Remote Similarity	NPD6370	Approved
0.621	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.621	Remote Similarity	NPD6009	Approved
0.619	Remote Similarity	NPD6319	Approved
0.6174	Remote Similarity	NPD7639	Approved
0.6174	Remote Similarity	NPD7640	Approved
0.6167	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6167	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD4820	Approved
0.6154	Remote Similarity	NPD4819	Approved
0.6154	Remote Similarity	NPD4822	Approved
0.6154	Remote Similarity	NPD4821	Approved
0.6148	Remote Similarity	NPD6882	Approved
0.6132	Remote Similarity	NPD5362	Discontinued
0.6126	Remote Similarity	NPD6411	Approved
0.6126	Remote Similarity	NPD7637	Suspended
0.6124	Remote Similarity	NPD7492	Approved
0.6117	Remote Similarity	NPD4271	Approved
0.6117	Remote Similarity	NPD4268	Approved
0.6098	Remote Similarity	NPD4632	Approved
0.609	Remote Similarity	NPD7260	Phase 2
0.6087	Remote Similarity	NPD7638	Approved
0.6083	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6082	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6077	Remote Similarity	NPD6616	Approved
0.6063	Remote Similarity	NPD6054	Approved
0.6038	Remote Similarity	NPD6435	Approved
0.6036	Remote Similarity	NPD5785	Approved
0.6031	Remote Similarity	NPD8293	Discontinued
0.6031	Remote Similarity	NPD7078	Approved
0.6017	Remote Similarity	NPD1407	Approved
0.6016	Remote Similarity	NPD8297	Approved
0.6016	Remote Similarity	NPD6016	Approved
0.6016	Remote Similarity	NPD6015	Approved
0.5984	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.5969	Remote Similarity	NPD5988	Approved
0.5963	Remote Similarity	NPD5786	Approved
0.5954	Remote Similarity	NPD8273	Phase 1
0.5888	Remote Similarity	NPD5209	Approved
0.5888	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.5872	Remote Similarity	NPD5363	Approved
0.5868	Remote Similarity	NPD5697	Approved
0.5854	Remote Similarity	NPD6421	Discontinued
0.5849	Remote Similarity	NPD4252	Approved
0.5849	Remote Similarity	NPD5368	Approved
0.582	Remote Similarity	NPD6899	Approved
0.582	Remote Similarity	NPD6881	Approved
0.5814	Remote Similarity	NPD6059	Approved
0.581	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD6649	Approved
0.5806	Remote Similarity	NPD2204	Approved
0.5806	Remote Similarity	NPD6650	Approved
0.5797	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.5782	Remote Similarity	NPD8389	Clinical (unspecified phase)
0.5772	Remote Similarity	NPD6012	Approved
0.5772	Remote Similarity	NPD6014	Approved
0.5772	Remote Similarity	NPD6013	Approved
0.5769	Remote Similarity	NPD5983	Phase 2
0.5766	Remote Similarity	NPD7524	Approved
0.5758	Remote Similarity	NPD898	Approved
0.5758	Remote Similarity	NPD897	Approved
0.5758	Remote Similarity	NPD896	Approved
0.5746	Remote Similarity	NPD8337	Approved
0.5746	Remote Similarity	NPD8336	Approved
0.5741	Remote Similarity	NPD4270	Approved
0.5741	Remote Similarity	NPD7685	Pre-registration
0.5741	Remote Similarity	NPD4269	Approved
0.5738	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.5727	Remote Similarity	NPD1694	Approved
0.5727	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5726	Remote Similarity	NPD7102	Approved
0.5726	Remote Similarity	NPD7290	Approved
0.5726	Remote Similarity	NPD6883	Approved
0.5725	Remote Similarity	NPD8415	Approved
0.5703	Remote Similarity	NPD7500	Approved
0.5693	Remote Similarity	NPD6845	Suspended
0.5693	Remote Similarity	NPD8338	Approved
0.5691	Remote Similarity	NPD6011	Approved
0.5688	Remote Similarity	NPD5332	Approved
0.5688	Remote Similarity	NPD5331	Approved
0.5682	Remote Similarity	NPD7604	Phase 2
0.568	Remote Similarity	NPD7116	Clinical (unspecified phase)
0.568	Remote Similarity	NPD6869	Approved
0.568	Remote Similarity	NPD6617	Approved
0.568	Remote Similarity	NPD6847	Approved
0.568	Remote Similarity	NPD8130	Phase 1
0.5667	Remote Similarity	NPD7632	Discontinued
0.5667	Remote Similarity	NPD5211	Phase 2
0.5656	Remote Similarity	NPD7128	Approved
0.5656	Remote Similarity	NPD6675	Approved
0.5656	Remote Similarity	NPD5739	Approved
0.5656	Remote Similarity	NPD6402	Approved
0.5649	Remote Similarity	NPD6921	Approved
0.5649	Remote Similarity	NPD8268	Approved
0.5649	Remote Similarity	NPD8269	Approved
0.5649	Remote Similarity	NPD8266	Approved
0.5649	Remote Similarity	NPD8267	Approved
0.5648	Remote Similarity	NPD5369	Approved
0.5648	Remote Similarity	NPD4790	Discontinued
0.5645	Remote Similarity	NPD6372	Approved
0.5645	Remote Similarity	NPD6373	Approved
0.5641	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5636	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD7266	Discontinued
0.5614	Remote Similarity	NPD8522	Clinical (unspecified phase)
0.561	Remote Similarity	NPD5701	Approved
0.5607	Remote Similarity	NPD7329	Approved
0.56	Remote Similarity	NPD4634	Approved

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