NPASS Compound

Structure

NPC284929 OpenBabel07101718282D 37 40 0 0 1 0 0 0 0 0999 V2000 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6665 -1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0029 -1.7213 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6720 -0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 2 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 0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 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 -0.8660 1.5000 0.0000 C 0 0 2 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 -2.5981 0.5000 0.0000 C 0 0 1 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 -0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3119 -2.6723 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 1.7321 2.0000 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 -0.0000 3.0000 0.0000 O 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 -1.7321 2.0000 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 -5.1962 3.0000 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 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 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 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 32 1 0 0 0 0 3 4 1 0 0 0 0 3 9 2 0 0 0 0 5 9 1 0 0 0 0 5 24 1 0 0 0 0 6 11 2 0 0 0 0 6 33 1 0 0 0 0 7 34 1 0 0 0 0 8 1 1 6 0 0 0 8 14 1 0 0 0 0 8 35 1 0 0 0 0 10 4 1 6 0 0 0 10 11 1 0 0 0 0 10 13 1 0 0 0 0 11 20 1 0 0 0 0 12 7 1 1 0 0 0 12 15 1 0 0 0 0 12 36 1 0 0 0 0 13 9 1 6 0 0 0 13 21 1 0 0 0 0 14 16 1 0 0 0 0 14 25 1 1 0 0 0 15 17 1 0 0 0 0 15 26 1 6 0 0 0 16 18 1 0 0 0 0 16 27 1 6 0 0 0 17 19 1 0 0 0 0 17 28 1 1 0 0 0 18 22 1 0 0 0 0 18 29 1 6 0 0 0 19 23 1 0 0 0 0 19 30 1 6 0 0 0 20 31 2 0 0 0 0 20 32 1 0 0 0 0 21 33 1 0 0 0 0 21 37 1 1 0 0 0 22 34 1 1 0 0 0 22 35 1 0 0 0 0 23 36 1 0 0 0 0 23 37 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	534.19
Volume:	487.292
LogP:	-0.249
LogD:	-0.552
LogS:	-1.438
# Rotatable Bonds:	8
TPSA:	214.06
# H-Bond Aceptor:	14
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.125
Synthetic Accessibility Score:	5.161
Fsp3:	0.783
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.297
MDCK Permeability:	0.00019346780027262866
Pgp-inhibitor:	0.0
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.9
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.188
Plasma Protein Binding (PPB):	28.882028579711914%
Volume Distribution (VD):	0.406
Pgp-substrate:	44.88985061645508%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.056
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.147
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.014
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.077
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.032

ADMET: Excretion

Clearance (CL):	1.025
Half-life (T1/2):	0.818

ADMET: Toxicity

hERG Blockers:	0.026
Human Hepatotoxicity (H-HT):	0.129
Drug-inuced Liver Injury (DILI):	0.924
AMES Toxicity:	0.274
Rat Oral Acute Toxicity:	0.453
Maximum Recommended Daily Dose:	0.032
Skin Sensitization:	0.57
Carcinogencity:	0.785
Eye Corrosion:	0.003
Eye Irritation:	0.121
Respiratory Toxicity:	0.938

Download Data

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

Natural Product: NPC284929

Natural Product ID:	NPC284929
*Common Name:**	Genipin 1-O-Alpha-L-Rhamnopyranosyl(1->6)-Beta-D-Glucopyranoside
IUPAC Name:	methyl (1S,4aS,7aS)-7-(hydroxymethyl)-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-2-yl]oxy-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
Synonyms:
Standard InCHIKey:	ZMBIVWMXUPESGV-JXGQDRBRSA-N
Standard InCHI:	InChI=1S/C23H34O14/c1-8-14(25)16(27)18(29)22(35-8)34-7-12-15(26)17(28)19(30)23(36-12)37-21-13-9(5-24)3-4-10(13)11(6-33-21)20(31)32-2/h3,6,8,10,12-19,21-30H,4-5,7H2,1-2H3/t8-,10+,12+,13+,14-,15+,16+,17-,18+,19+,21-,22+,23-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)O[C@H]2[C@@H]3C(=CC[C@@H]3C(=CO2)C(=O)OC)CO)O)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL463844
PubChem CID:	24878902
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
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]
NPO21315	Adina polycephala	Species	Rubiaceae	Eukaryota	bark	n.a.	n.a.	PMID[18303851]
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]
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]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9518	Gardenia jasminoides	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]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21315	Adina polycephala	Species	Rubiaceae	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	1
Others	1

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	100000.0	nM	PMID[570142]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	44.8	%	PMID[570141]

☑ 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 NPC284929 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	210
0.1-0.2	1304
0.2-0.3	4512
0.3-0.4	8574
0.4-0.5	14028
0.5-0.6	9048
0.6-0.7	4522
0.7-0.8	427
0.8-0.85	26
0.85-0.9	25
0.9-0.95	12
0.95-1	9

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC197541
1.0	High Similarity	NPC267869
1.0	High Similarity	NPC118761
1.0	High Similarity	NPC234304
0.9895	High Similarity	NPC222062
0.9684	High Similarity	NPC22149
0.9684	High Similarity	NPC255677
0.9684	High Similarity	NPC306344
0.9583	High Similarity	NPC28304
0.9583	High Similarity	NPC298255
0.949	High Similarity	NPC86095
0.9368	High Similarity	NPC241911
0.9286	High Similarity	NPC261117
0.9286	High Similarity	NPC310804
0.9286	High Similarity	NPC250545
0.9091	High Similarity	NPC13171
0.9091	High Similarity	NPC195510
0.8866	High Similarity	NPC469543
0.8854	High Similarity	NPC61201
0.875	High Similarity	NPC472126
0.875	High Similarity	NPC472124
0.875	High Similarity	NPC472125
0.8646	High Similarity	NPC470573
0.8646	High Similarity	NPC216826
0.8646	High Similarity	NPC6414
0.8646	High Similarity	NPC303451
0.8646	High Similarity	NPC307699
0.8646	High Similarity	NPC65665
0.8646	High Similarity	NPC120021
0.8646	High Similarity	NPC231710
0.8646	High Similarity	NPC270908
0.8558	High Similarity	NPC254538
0.8558	High Similarity	NPC474285
0.8485	Intermediate Similarity	NPC170204
0.8485	Intermediate Similarity	NPC101051
0.8469	Intermediate Similarity	NPC280390
0.8454	Intermediate Similarity	NPC117596
0.8431	Intermediate Similarity	NPC20673
0.835	Intermediate Similarity	NPC471599
0.8333	Intermediate Similarity	NPC244878
0.8333	Intermediate Similarity	NPC142583
0.8252	Intermediate Similarity	NPC219038
0.8235	Intermediate Similarity	NPC151093
0.8105	Intermediate Similarity	NPC188717
0.8105	Intermediate Similarity	NPC211455
0.8095	Intermediate Similarity	NPC475928
0.8077	Intermediate Similarity	NPC98859
0.8077	Intermediate Similarity	NPC4637
0.8039	Intermediate Similarity	NPC161293
0.8039	Intermediate Similarity	NPC306041
0.8021	Intermediate Similarity	NPC220167
0.8021	Intermediate Similarity	NPC136699
0.8	Intermediate Similarity	NPC106668
0.8	Intermediate Similarity	NPC177013
0.8	Intermediate Similarity	NPC35185
0.8	Intermediate Similarity	NPC4899
0.8	Intermediate Similarity	NPC474730
0.7944	Intermediate Similarity	NPC170432
0.7925	Intermediate Similarity	NPC27687
0.7925	Intermediate Similarity	NPC37240
0.7921	Intermediate Similarity	NPC472195
0.7921	Intermediate Similarity	NPC320552
0.7921	Intermediate Similarity	NPC472196
0.7921	Intermediate Similarity	NPC238090
0.7905	Intermediate Similarity	NPC287539
0.7905	Intermediate Similarity	NPC3488
0.79	Intermediate Similarity	NPC327253
0.7885	Intermediate Similarity	NPC40182
0.7885	Intermediate Similarity	NPC198422
0.7885	Intermediate Similarity	NPC472015
0.787	Intermediate Similarity	NPC148270
0.787	Intermediate Similarity	NPC80338
0.787	Intermediate Similarity	NPC197813
0.7864	Intermediate Similarity	NPC54731
0.7843	Intermediate Similarity	NPC294293
0.7843	Intermediate Similarity	NPC159698
0.7835	Intermediate Similarity	NPC266718
0.783	Intermediate Similarity	NPC201191
0.7822	Intermediate Similarity	NPC477749
0.7822	Intermediate Similarity	NPC9447
0.7822	Intermediate Similarity	NPC472197
0.7798	Intermediate Similarity	NPC110701
0.7798	Intermediate Similarity	NPC392
0.7798	Intermediate Similarity	NPC219900
0.7798	Intermediate Similarity	NPC177524
0.7788	Intermediate Similarity	NPC472290
0.7778	Intermediate Similarity	NPC127235
0.7759	Intermediate Similarity	NPC473228
0.7759	Intermediate Similarity	NPC470829
0.7757	Intermediate Similarity	NPC197736
0.7755	Intermediate Similarity	NPC470124
0.7714	Intermediate Similarity	NPC124181
0.7714	Intermediate Similarity	NPC473307
0.77	Intermediate Similarity	NPC137368
0.767	Intermediate Similarity	NPC63897
0.7658	Intermediate Similarity	NPC193741
0.7653	Intermediate Similarity	NPC475035
0.7652	Intermediate Similarity	NPC13710
0.7652	Intermediate Similarity	NPC475309
0.7647	Intermediate Similarity	NPC472199
0.7642	Intermediate Similarity	NPC473146
0.7636	Intermediate Similarity	NPC473807
0.7624	Intermediate Similarity	NPC249408
0.7624	Intermediate Similarity	NPC104129
0.7624	Intermediate Similarity	NPC477748
0.7619	Intermediate Similarity	NPC153559
0.7604	Intermediate Similarity	NPC163362
0.7604	Intermediate Similarity	NPC127295
0.76	Intermediate Similarity	NPC475186
0.76	Intermediate Similarity	NPC118077
0.76	Intermediate Similarity	NPC475037
0.7596	Intermediate Similarity	NPC241407
0.7596	Intermediate Similarity	NPC291709
0.7576	Intermediate Similarity	NPC470658
0.7573	Intermediate Similarity	NPC320089
0.757	Intermediate Similarity	NPC476611
0.7568	Intermediate Similarity	NPC315836
0.7568	Intermediate Similarity	NPC313668
0.7563	Intermediate Similarity	NPC318135
0.7549	Intermediate Similarity	NPC202886
0.7547	Intermediate Similarity	NPC90819
0.7544	Intermediate Similarity	NPC472274
0.7524	Intermediate Similarity	NPC143446
0.7524	Intermediate Similarity	NPC256230
0.7522	Intermediate Similarity	NPC475851
0.7522	Intermediate Similarity	NPC475924
0.75	Intermediate Similarity	NPC323472
0.75	Intermediate Similarity	NPC83005
0.75	Intermediate Similarity	NPC304163
0.75	Intermediate Similarity	NPC256368
0.75	Intermediate Similarity	NPC475927
0.75	Intermediate Similarity	NPC472198
0.75	Intermediate Similarity	NPC475832
0.75	Intermediate Similarity	NPC2003
0.75	Intermediate Similarity	NPC71589
0.75	Intermediate Similarity	NPC25701
0.7458	Intermediate Similarity	NPC170084
0.7458	Intermediate Similarity	NPC202051
0.7458	Intermediate Similarity	NPC476204
0.7458	Intermediate Similarity	NPC170880
0.7456	Intermediate Similarity	NPC264153
0.7456	Intermediate Similarity	NPC474410
0.7456	Intermediate Similarity	NPC293658
0.7455	Intermediate Similarity	NPC476740
0.7455	Intermediate Similarity	NPC41681
0.7455	Intermediate Similarity	NPC476738
0.7453	Intermediate Similarity	NPC476612
0.7453	Intermediate Similarity	NPC476613
0.7451	Intermediate Similarity	NPC285588
0.7436	Intermediate Similarity	NPC122971
0.7436	Intermediate Similarity	NPC219656
0.7434	Intermediate Similarity	NPC126897
0.7434	Intermediate Similarity	NPC297945
0.7431	Intermediate Similarity	NPC309398
0.7429	Intermediate Similarity	NPC6765
0.7429	Intermediate Similarity	NPC93869
0.7429	Intermediate Similarity	NPC36954
0.7414	Intermediate Similarity	NPC474483
0.7411	Intermediate Similarity	NPC118225
0.7407	Intermediate Similarity	NPC475157
0.7407	Intermediate Similarity	NPC2313
0.7407	Intermediate Similarity	NPC471637
0.7407	Intermediate Similarity	NPC154132
0.7407	Intermediate Similarity	NPC475655
0.7407	Intermediate Similarity	NPC57586
0.74	Intermediate Similarity	NPC477747
0.74	Intermediate Similarity	NPC475034
0.74	Intermediate Similarity	NPC477746
0.7398	Intermediate Similarity	NPC213634
0.7391	Intermediate Similarity	NPC181145
0.7383	Intermediate Similarity	NPC169468
0.7383	Intermediate Similarity	NPC81483
0.7383	Intermediate Similarity	NPC61630
0.7383	Intermediate Similarity	NPC307517
0.7379	Intermediate Similarity	NPC118078
0.7377	Intermediate Similarity	NPC245094
0.7374	Intermediate Similarity	NPC142111
0.7374	Intermediate Similarity	NPC473315
0.7373	Intermediate Similarity	NPC48692
0.7373	Intermediate Similarity	NPC470312
0.7364	Intermediate Similarity	NPC469869
0.7353	Intermediate Similarity	NPC470137
0.7353	Intermediate Similarity	NPC248312
0.7339	Intermediate Similarity	NPC80144
0.7339	Intermediate Similarity	NPC155529
0.7333	Intermediate Similarity	NPC477345
0.7333	Intermediate Similarity	NPC219804
0.7333	Intermediate Similarity	NPC274588
0.7333	Intermediate Similarity	NPC477348
0.7333	Intermediate Similarity	NPC238264
0.7328	Intermediate Similarity	NPC207637
0.7321	Intermediate Similarity	NPC193765
0.7321	Intermediate Similarity	NPC475960
0.732	Intermediate Similarity	NPC321728
0.7311	Intermediate Similarity	NPC183353
0.7311	Intermediate Similarity	NPC233500
0.7311	Intermediate Similarity	NPC469812
0.7308	Intermediate Similarity	NPC473150
0.7308	Intermediate Similarity	NPC473321
0.7308	Intermediate Similarity	NPC294643

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 NPC284929 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	1550
0.2-0.3	3862
0.3-0.4	2362
0.4-0.5	819
0.5-0.6	305
0.6-0.7	74
0.7-0.8	6
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
0.7798	Intermediate Similarity	NPD6686	Approved
0.7458	Intermediate Similarity	NPD8513	Phase 3
0.7434	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7383	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7379	Intermediate Similarity	NPD6698	Approved
0.7379	Intermediate Similarity	NPD46	Approved
0.7311	Intermediate Similarity	NPD8517	Approved
0.7311	Intermediate Similarity	NPD8515	Approved
0.7311	Intermediate Similarity	NPD8516	Approved
0.7167	Intermediate Similarity	NPD7503	Approved
0.7073	Intermediate Similarity	NPD7507	Approved
0.6923	Remote Similarity	NPD6053	Discontinued
0.6905	Remote Similarity	NPD7319	Approved
0.6885	Remote Similarity	NPD8033	Approved
0.6822	Remote Similarity	NPD7983	Approved
0.6803	Remote Similarity	NPD8377	Approved
0.6803	Remote Similarity	NPD8294	Approved
0.6783	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6783	Remote Similarity	NPD6412	Phase 2
0.6777	Remote Similarity	NPD7328	Approved
0.6777	Remote Similarity	NPD7327	Approved
0.6774	Remote Similarity	NPD7830	Approved
0.6774	Remote Similarity	NPD7829	Approved
0.6762	Remote Similarity	NPD4250	Approved
0.6762	Remote Similarity	NPD4251	Approved
0.6752	Remote Similarity	NPD6371	Approved
0.6748	Remote Similarity	NPD8296	Approved
0.6748	Remote Similarity	NPD8380	Approved
0.6748	Remote Similarity	NPD8335	Approved
0.6748	Remote Similarity	NPD8379	Approved
0.6748	Remote Similarity	NPD8378	Approved
0.6746	Remote Similarity	NPD8074	Phase 3
0.6729	Remote Similarity	NPD7838	Discovery
0.6723	Remote Similarity	NPD8133	Approved
0.6721	Remote Similarity	NPD7516	Approved
0.6699	Remote Similarity	NPD6110	Phase 1
0.6699	Remote Similarity	NPD7154	Phase 3
0.6667	Remote Similarity	NPD4249	Approved
0.6635	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD7839	Suspended
0.6423	Remote Similarity	NPD7115	Discovery
0.6423	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6408	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6406	Remote Similarity	NPD8451	Approved
0.6404	Remote Similarity	NPD7639	Approved
0.6404	Remote Similarity	NPD7640	Approved
0.6381	Remote Similarity	NPD5362	Discontinued
0.6378	Remote Similarity	NPD7642	Approved
0.6378	Remote Similarity	NPD8328	Phase 3
0.6371	Remote Similarity	NPD7641	Discontinued
0.6364	Remote Similarity	NPD7637	Suspended
0.6357	Remote Similarity	NPD8448	Approved
0.6349	Remote Similarity	NPD8444	Approved
0.6348	Remote Similarity	NPD5344	Discontinued
0.6336	Remote Similarity	NPD8392	Approved
0.6336	Remote Similarity	NPD8391	Approved
0.6336	Remote Similarity	NPD8390	Approved
0.6328	Remote Similarity	NPD8341	Approved
0.6328	Remote Similarity	NPD8299	Approved
0.6328	Remote Similarity	NPD8342	Approved
0.6328	Remote Similarity	NPD8340	Approved
0.6316	Remote Similarity	NPD4225	Approved
0.6316	Remote Similarity	NPD7638	Approved
0.6306	Remote Similarity	NPD5778	Approved
0.6306	Remote Similarity	NPD5779	Approved
0.6299	Remote Similarity	NPD8080	Discontinued
0.629	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.625	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.622	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6214	Remote Similarity	NPD4268	Approved
0.6214	Remote Similarity	NPD4271	Approved
0.6183	Remote Similarity	NPD8337	Approved
0.6183	Remote Similarity	NPD7736	Approved
0.6183	Remote Similarity	NPD8336	Approved
0.6182	Remote Similarity	NPD1695	Approved
0.6172	Remote Similarity	NPD6370	Approved
0.6126	Remote Similarity	NPD5785	Approved
0.6111	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6111	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.6107	Remote Similarity	NPD8293	Discontinued
0.6098	Remote Similarity	NPD6882	Approved
0.6095	Remote Similarity	NPD4820	Approved
0.6095	Remote Similarity	NPD4822	Approved
0.6095	Remote Similarity	NPD4819	Approved
0.6095	Remote Similarity	NPD4821	Approved
0.6077	Remote Similarity	NPD7492	Approved
0.6058	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6058	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.6053	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6045	Remote Similarity	NPD7260	Phase 2
0.6036	Remote Similarity	NPD6101	Approved
0.6036	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6032	Remote Similarity	NPD6009	Approved
0.6031	Remote Similarity	NPD6616	Approved
0.6016	Remote Similarity	NPD6319	Approved
0.6016	Remote Similarity	NPD6054	Approved
0.5985	Remote Similarity	NPD7078	Approved
0.5984	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5983	Remote Similarity	NPD6648	Approved
0.5981	Remote Similarity	NPD6435	Approved
0.5968	Remote Similarity	NPD8297	Approved
0.5966	Remote Similarity	NPD1407	Approved
0.5965	Remote Similarity	NPD5282	Discontinued
0.5963	Remote Similarity	NPD5363	Approved
0.5943	Remote Similarity	NPD4252	Approved
0.5929	Remote Similarity	NPD6411	Approved
0.5926	Remote Similarity	NPD5332	Approved
0.5926	Remote Similarity	NPD5331	Approved
0.592	Remote Similarity	NPD4632	Approved
0.5909	Remote Similarity	NPD5786	Approved
0.5891	Remote Similarity	NPD6059	Approved
0.5888	Remote Similarity	NPD4790	Discontinued
0.5882	Remote Similarity	NPD7632	Discontinued
0.5882	Remote Similarity	NPD8338	Approved
0.5877	Remote Similarity	NPD6399	Phase 3
0.587	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.5859	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5856	Remote Similarity	NPD7524	Approved
0.5849	Remote Similarity	NPD7329	Approved
0.5846	Remote Similarity	NPD6016	Approved
0.5846	Remote Similarity	NPD6015	Approved
0.5833	Remote Similarity	NPD4270	Approved
0.5833	Remote Similarity	NPD4269	Approved
0.5806	Remote Similarity	NPD6421	Discontinued
0.5806	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.5802	Remote Similarity	NPD5988	Approved
0.5794	Remote Similarity	NPD5368	Approved
0.5772	Remote Similarity	NPD6899	Approved
0.5772	Remote Similarity	NPD6881	Approved
0.5772	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5766	Remote Similarity	NPD6845	Suspended
0.576	Remote Similarity	NPD6650	Approved
0.576	Remote Similarity	NPD6649	Approved
0.5738	Remote Similarity	NPD6675	Approved
0.5738	Remote Similarity	NPD5739	Approved
0.5738	Remote Similarity	NPD7128	Approved
0.5738	Remote Similarity	NPD6402	Approved
0.5727	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5726	Remote Similarity	NPD6372	Approved
0.5726	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5726	Remote Similarity	NPD6373	Approved
0.5725	Remote Similarity	NPD8266	Approved
0.5725	Remote Similarity	NPD8268	Approved
0.5725	Remote Similarity	NPD8267	Approved
0.5725	Remote Similarity	NPD8269	Approved
0.5706	Remote Similarity	NPD7685	Pre-registration
0.5694	Remote Similarity	NPD7266	Discontinued
0.5691	Remote Similarity	NPD5697	Approved
0.5688	Remote Similarity	NPD5209	Approved
0.5688	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.5683	Remote Similarity	NPD8415	Approved
0.568	Remote Similarity	NPD6883	Approved
0.568	Remote Similarity	NPD7102	Approved
0.568	Remote Similarity	NPD7290	Approved
0.5678	Remote Similarity	NPD6084	Phase 2
0.5678	Remote Similarity	NPD6083	Phase 2
0.5672	Remote Similarity	NPD8273	Phase 1
0.5659	Remote Similarity	NPD7500	Approved
0.5656	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.5648	Remote Similarity	NPD7332	Phase 2
0.5645	Remote Similarity	NPD7320	Approved
0.5639	Remote Similarity	NPD6067	Discontinued
0.5639	Remote Similarity	NPD7604	Phase 2
0.5638	Remote Similarity	NPD8389	Clinical (unspecified phase)
0.5636	Remote Similarity	NPD6695	Phase 3
0.5635	Remote Similarity	NPD2204	Approved
0.5635	Remote Similarity	NPD7116	Clinical (unspecified phase)
0.5635	Remote Similarity	NPD6847	Approved
0.5635	Remote Similarity	NPD8130	Phase 1
0.5635	Remote Similarity	NPD6617	Approved
0.5635	Remote Similarity	NPD6869	Approved
0.561	Remote Similarity	NPD6640	Phase 3
0.5606	Remote Similarity	NPD5983	Phase 2
0.56	Remote Similarity	NPD6012	Approved
0.56	Remote Similarity	NPD6014	Approved
0.56	Remote Similarity	NPD6013	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