NPASS Compound

Structure

CID45959 OpenBabel06191715382D 57 63 0 0 1 0 0 0 0 0999 V2000 6.5580 0.5742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5712 1.9324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8421 -1.0991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3267 -1.9385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8394 -2.4231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8394 1.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9639 0.1013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5077 -0.4406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8394 -1.4538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5181 -0.4846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5181 -3.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6788 -2.9077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6788 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3544 0.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2399 1.1190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2015 0.9481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5544 -7.2692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5181 -6.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7739 0.0045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6725 0.9685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8394 -0.4846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1654 1.0494 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.5544 -6.3000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3575 -5.8154 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5181 -1.4538 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8394 -1.4538 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3575 -2.9077 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5597 0.1639 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3938 -5.8154 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1969 -6.3000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3938 -4.8462 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0363 -5.8154 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5544 -4.3615 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0363 -4.8462 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7150 -4.8462 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1969 -4.3615 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3575 -1.9385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6788 -1.9385 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8394 -0.4846 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4558 -0.2391 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8884 0.3988 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.3938 -7.7538 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5181 -7.2692 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8752 -0.9594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6501 1.8887 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.2332 -6.3000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1969 -7.2692 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.2332 -4.3615 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8756 -6.3000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5544 -3.3923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7150 -5.8154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3575 -4.8462 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1969 -3.3923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8756 -4.3615 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4038 -0.4406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 21 1 0 0 0 0 3 38 1 0 0 0 0 4 38 1 0 0 0 0 6 40 1 0 0 0 0 9 10 1 0 0 0 0 9 22 1 0 0 0 0 10 27 1 0 0 0 0 11 14 1 0 0 0 0 11 26 1 0 0 0 0 12 13 1 0 0 0 0 12 28 1 0 0 0 0 13 39 1 0 0 0 0 14 40 1 0 0 0 0 15 16 1 0 0 0 0 15 42 1 0 0 0 0 16 43 1 0 0 0 0 17 23 1 0 0 0 0 17 41 1 0 0 0 0 18 44 1 0 0 0 0 19 45 1 0 0 0 0 20 46 1 0 0 0 0 21 43 1 0 0 0 0 22 29 1 0 0 0 0 22 41 1 1 0 0 0 23 29 1 0 0 0 0 23 47 1 1 0 0 0 24 18 1 6 0 0 0 24 30 1 0 0 0 0 24 53 1 0 0 0 0 25 19 1 6 0 0 0 25 31 1 0 0 0 0 25 54 1 0 0 0 0 26 38 1 0 0 0 0 26 39 1 6 0 0 0 27 39 1 6 0 0 0 27 40 1 0 0 0 0 28 38 1 0 0 0 0 28 55 1 6 0 0 0 29 42 1 6 0 0 0 30 32 1 0 0 0 0 30 48 1 1 0 0 0 31 33 1 0 0 0 0 31 49 1 1 0 0 0 32 34 1 0 0 0 0 32 50 1 6 0 0 0 33 35 1 0 0 0 0 33 51 1 6 0 0 0 34 36 1 0 0 0 0 34 52 1 1 0 0 0 35 37 1 0 0 0 0 35 56 1 1 0 0 0 36 53 1 0 0 0 0 36 56 1 6 0 0 0 37 54 1 0 0 0 0 37 55 1 6 0 0 0 39 5 1 6 0 0 0 40 41 1 1 0 0 0 41 7 1 1 0 0 0 42 8 1 1 0 0 0 42 57 1 0 0 0 0 43 20 1 6 0 0 0 43 57 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	814.51
Volume:	815.452
LogP:	2.934
LogD:	3.449
LogS:	-3.138
# Rotatable Bonds:	9
TPSA:	228.22
# H-Bond Aceptor:	14
# H-Bond Donor:	9
# Rings:	7
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.151
Synthetic Accessibility Score:	6.073
Fsp3:	1.0
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:	-5.543
MDCK Permeability:	6.699997175019234e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.324
20% Bioavailability (F20%):	0.288
30% Bioavailability (F30%):	0.782

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	79.63103485107422%
Volume Distribution (VD):	0.22
Pgp-substrate:	7.044830799102783%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.344
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.72
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.016
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.077
CYP3A4-inhibitor:	0.094
CYP3A4-substrate:	0.127

ADMET: Excretion

Clearance (CL):	0.955
Half-life (T1/2):	0.692

ADMET: Toxicity

hERG Blockers:	0.191
Human Hepatotoxicity (H-HT):	0.208
Drug-inuced Liver Injury (DILI):	0.009
AMES Toxicity:	0.074
Rat Oral Acute Toxicity:	0.077
Maximum Recommended Daily Dose:	0.039
Skin Sensitization:	0.664
Carcinogencity:	0.008
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.743

Download Data

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

Natural Product: NPC45959

Natural Product ID:	NPC45959
*Common Name:**	Operculinoside A
IUPAC Name:	(2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-2-[[(3S,5R,8R,9R,10R,13R,14R,16R,17R)-16-hydroxy-17-[(2S,5S)-5-(hydroxymethyl)-2-methyl-5-propan-2-yloxolan-2-yl]-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]-6-(hydroxymethyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:	Operculinoside A
Standard InCHIKey:	WSPSRBVXDVGFMA-LJGRZBPHSA-N
Standard InCHI:	InChI=1S/C43H74O14/c1-21(2)43(20-46)16-15-42(8,57-43)29-22-9-10-27-39(5)13-12-28(38(3,4)26(39)11-14-40(27,6)41(22,7)17-23(29)47)55-37-35(33(51)31(49)25(19-45)54-37)56-36-34(52)32(50)30(48)24(18-44)53-36/h21-37,44-52H,9-20H2,1-8H3/t22-,23-,24-,25-,26+,27-,28+,29-,30-,31-,32+,33+,34-,35-,36+,37+,39+,40-,41-,42+,43-/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3CC[C@H]3[C@@]2(C)C[C@H]([C@@H]3[C@]2(C)CC[C@@](O2)(CO)C(C)C)O)C)C)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1910785
PubChem CID:	54671472
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO10224	Operculina turpethum	Species	Convolvulaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21866900]
NPO10224	Operculina turpethum	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
Others	4

Activity Type	# Activity
NON-MOLECULAR	3
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	46.7	%	PMID[545517]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	-14.7	%	PMID[545517]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	-22.8	%	PMID[545517]
NPT27	Others	Unspecified		MTD	=	12.5	ug ml-1	PMID[545517]

☑ 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 NPC45959 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	587
0.1-0.2	5160
0.2-0.3	14011
0.3-0.4	10304
0.4-0.5	5516
0.5-0.6	3611
0.6-0.7	1930
0.7-0.8	1054
0.8-0.85	252
0.85-0.9	109
0.9-0.95	56
0.95-1	107

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC252253
0.9885	High Similarity	NPC149400
0.9885	High Similarity	NPC144790
0.9885	High Similarity	NPC88962
0.9775	High Similarity	NPC476510
0.9775	High Similarity	NPC139271
0.9775	High Similarity	NPC142264
0.9775	High Similarity	NPC304011
0.9773	High Similarity	NPC473774
0.9773	High Similarity	NPC24960
0.9773	High Similarity	NPC291547
0.9773	High Similarity	NPC174024
0.9773	High Similarity	NPC253268
0.9773	High Similarity	NPC179859
0.9773	High Similarity	NPC475436
0.9773	High Similarity	NPC312678
0.9773	High Similarity	NPC131693
0.9773	High Similarity	NPC473851
0.977	High Similarity	NPC229801
0.977	High Similarity	NPC307167
0.977	High Similarity	NPC210759
0.9667	High Similarity	NPC470028
0.9667	High Similarity	NPC233649
0.9667	High Similarity	NPC477222
0.9667	High Similarity	NPC477223
0.9663	High Similarity	NPC474399
0.9659	High Similarity	NPC311246
0.9659	High Similarity	NPC477451
0.9659	High Similarity	NPC177834
0.9659	High Similarity	NPC249204
0.9659	High Similarity	NPC234352
0.9659	High Similarity	NPC141769
0.9659	High Similarity	NPC167644
0.9659	High Similarity	NPC477547
0.9659	High Similarity	NPC250393
0.9659	High Similarity	NPC297348
0.9659	High Similarity	NPC325828
0.9659	High Similarity	NPC48339
0.9655	High Similarity	NPC65550
0.9655	High Similarity	NPC473542
0.9556	High Similarity	NPC121453
0.9551	High Similarity	NPC309866
0.9551	High Similarity	NPC113500
0.9551	High Similarity	NPC471464
0.9551	High Similarity	NPC217205
0.9551	High Similarity	NPC175
0.9551	High Similarity	NPC305418
0.9551	High Similarity	NPC477224
0.9551	High Similarity	NPC222731
0.9551	High Similarity	NPC3538
0.9551	High Similarity	NPC264101
0.9551	High Similarity	NPC294686
0.9551	High Similarity	NPC291203
0.9545	High Similarity	NPC473830
0.9545	High Similarity	NPC149966
0.9545	High Similarity	NPC5632
0.9545	High Similarity	NPC204881
0.954	High Similarity	NPC82955
0.954	High Similarity	NPC131466
0.9451	High Similarity	NPC475207
0.9451	High Similarity	NPC476112
0.9451	High Similarity	NPC307534
0.9451	High Similarity	NPC274200
0.9444	High Similarity	NPC19400
0.9444	High Similarity	NPC107962
0.9444	High Similarity	NPC473064
0.9444	High Similarity	NPC473727
0.9444	High Similarity	NPC473610
0.9444	High Similarity	NPC6295
0.9444	High Similarity	NPC206003
0.9444	High Similarity	NPC473067
0.9444	High Similarity	NPC473065
0.9444	High Similarity	NPC211354
0.9444	High Similarity	NPC92196
0.9444	High Similarity	NPC475351
0.9444	High Similarity	NPC107188
0.9438	High Similarity	NPC137004
0.9438	High Similarity	NPC172838
0.9438	High Similarity	NPC473726
0.9432	High Similarity	NPC279329
0.9425	High Similarity	NPC281004
0.9355	High Similarity	NPC472081
0.9355	High Similarity	NPC475574
0.9355	High Similarity	NPC476512
0.9355	High Similarity	NPC108227
0.9348	High Similarity	NPC473616
0.9348	High Similarity	NPC473518
0.9341	High Similarity	NPC470865
0.9341	High Similarity	NPC473601
0.9341	High Similarity	NPC203434
0.9341	High Similarity	NPC128572
0.9341	High Similarity	NPC98018
0.9341	High Similarity	NPC470863
0.9341	High Similarity	NPC238796
0.9341	High Similarity	NPC475625
0.9341	High Similarity	NPC30856
0.9341	High Similarity	NPC470864
0.9341	High Similarity	NPC475643
0.9341	High Similarity	NPC195297
0.9341	High Similarity	NPC84111
0.9341	High Similarity	NPC132080
0.9341	High Similarity	NPC470866
0.9341	High Similarity	NPC184617
0.9341	High Similarity	NPC232037
0.9341	High Similarity	NPC237071
0.9341	High Similarity	NPC160426
0.9341	High Similarity	NPC287483
0.9341	High Similarity	NPC97700
0.9341	High Similarity	NPC284104
0.9341	High Similarity	NPC103616
0.9341	High Similarity	NPC116756
0.9326	High Similarity	NPC36372
0.9326	High Similarity	NPC293609
0.9318	High Similarity	NPC473472
0.9318	High Similarity	NPC20822
0.9318	High Similarity	NPC102725
0.931	High Similarity	NPC43912
0.931	High Similarity	NPC140446
0.9255	High Similarity	NPC470029
0.9255	High Similarity	NPC310138
0.9255	High Similarity	NPC114700
0.9255	High Similarity	NPC134967
0.9239	High Similarity	NPC470861
0.9239	High Similarity	NPC115165
0.9239	High Similarity	NPC51520
0.9239	High Similarity	NPC303069
0.9239	High Similarity	NPC83137
0.9239	High Similarity	NPC470862
0.9239	High Similarity	NPC232611
0.9222	High Similarity	NPC277774
0.9213	High Similarity	NPC223143
0.9158	High Similarity	NPC97260
0.9158	High Similarity	NPC476837
0.9158	High Similarity	NPC139181
0.914	High Similarity	NPC291548
0.914	High Similarity	NPC473638
0.913	High Similarity	NPC296936
0.9121	High Similarity	NPC30687
0.9121	High Similarity	NPC473503
0.9111	High Similarity	NPC476668
0.9111	High Similarity	NPC473637
0.9111	High Similarity	NPC59006
0.908	High Similarity	NPC290612
0.9032	High Similarity	NPC470591
0.9022	High Similarity	NPC469710
0.9022	High Similarity	NPC57964
0.9022	High Similarity	NPC477494
0.9022	High Similarity	NPC94582
0.9011	High Similarity	NPC476669
0.8947	High Similarity	NPC477225
0.8947	High Similarity	NPC476838
0.8947	High Similarity	NPC476839
0.8925	High Similarity	NPC473287
0.8913	High Similarity	NPC475325
0.8889	High Similarity	NPC228059
0.8876	High Similarity	NPC161928
0.8876	High Similarity	NPC210658
0.8876	High Similarity	NPC472396
0.8864	High Similarity	NPC273290
0.8864	High Similarity	NPC232044
0.8842	High Similarity	NPC470030
0.883	High Similarity	NPC210157
0.8804	High Similarity	NPC18724
0.8804	High Similarity	NPC470623
0.8804	High Similarity	NPC171741
0.8804	High Similarity	NPC323231
0.8804	High Similarity	NPC224003
0.8778	High Similarity	NPC128475
0.875	High Similarity	NPC227260
0.875	High Similarity	NPC477172
0.8736	High Similarity	NPC296734
0.8736	High Similarity	NPC470611
0.8723	High Similarity	NPC156377
0.871	High Similarity	NPC191915
0.871	High Similarity	NPC77717
0.871	High Similarity	NPC471373
0.871	High Similarity	NPC148593
0.871	High Similarity	NPC253611
0.871	High Similarity	NPC267238
0.871	High Similarity	NPC151214
0.8673	High Similarity	NPC475521
0.8646	High Similarity	NPC20028
0.8617	High Similarity	NPC471425
0.8617	High Similarity	NPC471424
0.8617	High Similarity	NPC189575
0.8617	High Similarity	NPC471429
0.8617	High Similarity	NPC205129
0.8617	High Similarity	NPC106701
0.8586	High Similarity	NPC215408
0.8556	High Similarity	NPC471240
0.8542	High Similarity	NPC292775
0.8539	High Similarity	NPC474156
0.8526	High Similarity	NPC472989
0.8526	High Similarity	NPC252056
0.8515	High Similarity	NPC476835
0.8506	High Similarity	NPC7479
0.8506	High Similarity	NPC248944
0.8506	High Similarity	NPC257296
0.85	High Similarity	NPC54619
0.8485	Intermediate Similarity	NPC475365

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 NPC45959 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	559
0.1-0.2	4650
0.2-0.3	2795
0.3-0.4	605
0.4-0.5	300
0.5-0.6	181
0.6-0.7	41
0.7-0.8	16
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9659	High Similarity	NPD8171	Discontinued
0.8673	High Similarity	NPD8170	Clinical (unspecified phase)
0.8506	High Similarity	NPD6928	Phase 2
0.7748	Intermediate Similarity	NPD8377	Approved
0.7748	Intermediate Similarity	NPD8294	Approved
0.7679	Intermediate Similarity	NPD8033	Approved
0.7679	Intermediate Similarity	NPD8335	Approved
0.7679	Intermediate Similarity	NPD8380	Approved
0.7679	Intermediate Similarity	NPD8296	Approved
0.7679	Intermediate Similarity	NPD8379	Approved
0.7679	Intermediate Similarity	NPD8378	Approved
0.7523	Intermediate Similarity	NPD8133	Approved
0.75	Intermediate Similarity	NPD7991	Discontinued
0.7411	Intermediate Similarity	NPD7327	Approved
0.7411	Intermediate Similarity	NPD7328	Approved
0.7356	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7345	Intermediate Similarity	NPD7516	Approved
0.7222	Intermediate Similarity	NPD1810	Approved
0.7222	Intermediate Similarity	NPD1811	Approved
0.6975	Remote Similarity	NPD7507	Approved
0.6923	Remote Similarity	NPD7503	Approved
0.6889	Remote Similarity	NPD2686	Approved
0.6889	Remote Similarity	NPD2687	Approved
0.6889	Remote Similarity	NPD2254	Approved
0.6847	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.6818	Remote Similarity	NPD6412	Phase 2
0.6803	Remote Similarity	NPD7319	Approved
0.6735	Remote Similarity	NPD3669	Approved
0.6735	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6724	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.6721	Remote Similarity	NPD7736	Approved
0.6703	Remote Similarity	NPD4787	Phase 1
0.664	Remote Similarity	NPD8449	Approved
0.6638	Remote Similarity	NPD6940	Discontinued
0.6607	Remote Similarity	NPD8174	Phase 2
0.6587	Remote Similarity	NPD8450	Suspended
0.6583	Remote Similarity	NPD6370	Approved
0.6562	Remote Similarity	NPD6118	Approved
0.6562	Remote Similarity	NPD6115	Approved
0.6562	Remote Similarity	NPD6697	Approved
0.6562	Remote Similarity	NPD6114	Approved
0.6522	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6504	Remote Similarity	NPD8293	Discontinued
0.6458	Remote Similarity	NPD6116	Phase 1
0.6417	Remote Similarity	NPD6054	Approved
0.6417	Remote Similarity	NPD6059	Approved
0.6404	Remote Similarity	NPD371	Approved
0.6393	Remote Similarity	NPD8328	Phase 3
0.6354	Remote Similarity	NPD6117	Approved
0.6263	Remote Similarity	NPD7525	Registered
0.623	Remote Similarity	NPD6016	Approved
0.623	Remote Similarity	NPD6015	Approved
0.621	Remote Similarity	NPD7492	Approved
0.6179	Remote Similarity	NPD5988	Approved
0.616	Remote Similarity	NPD6616	Approved
0.6146	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6131	Remote Similarity	NPD7625	Phase 1
0.6129	Remote Similarity	NPD6067	Discontinued
0.6111	Remote Similarity	NPD7078	Approved
0.6105	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.6105	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.6082	Remote Similarity	NPD3702	Approved
0.6082	Remote Similarity	NPD3703	Phase 2
0.6075	Remote Similarity	NPD8034	Phase 2
0.6075	Remote Similarity	NPD8035	Phase 2
0.6071	Remote Similarity	NPD1700	Approved
0.6053	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.6053	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.604	Remote Similarity	NPD1780	Approved
0.604	Remote Similarity	NPD1779	Approved
0.6034	Remote Similarity	NPD6686	Approved
0.6	Remote Similarity	NPD4244	Approved
0.6	Remote Similarity	NPD4245	Approved
0.5966	Remote Similarity	NPD6882	Approved
0.5966	Remote Similarity	NPD8297	Approved
0.5938	Remote Similarity	NPD6033	Approved
0.5902	Remote Similarity	NPD6009	Approved
0.5895	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.5895	Remote Similarity	NPD3698	Phase 2
0.5895	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.5893	Remote Similarity	NPD7638	Approved
0.5889	Remote Similarity	NPD6123	Approved
0.5887	Remote Similarity	NPD6319	Approved
0.5849	Remote Similarity	NPD7524	Approved
0.5842	Remote Similarity	NPD7645	Phase 2
0.5841	Remote Similarity	NPD7639	Approved
0.5841	Remote Similarity	NPD7640	Approved
0.584	Remote Similarity	NPD8513	Phase 3
0.584	Remote Similarity	NPD8516	Approved
0.584	Remote Similarity	NPD8515	Approved
0.584	Remote Similarity	NPD8517	Approved
0.581	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5795	Remote Similarity	NPD2267	Suspended
0.5789	Remote Similarity	NPD5360	Phase 3
0.5789	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.5785	Remote Similarity	NPD4632	Approved
0.5773	Remote Similarity	NPD5777	Approved
0.5763	Remote Similarity	NPD7320	Approved
0.5763	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5755	Remote Similarity	NPD8308	Discontinued
0.5739	Remote Similarity	NPD7632	Discontinued
0.5726	Remote Similarity	NPD6675	Approved
0.5726	Remote Similarity	NPD5739	Approved
0.5726	Remote Similarity	NPD7128	Approved
0.5726	Remote Similarity	NPD6402	Approved
0.5714	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD6373	Approved
0.5714	Remote Similarity	NPD6372	Approved
0.5688	Remote Similarity	NPD6701	Clinical (unspecified phase)
0.5688	Remote Similarity	NPD6700	Approved
0.5678	Remote Similarity	NPD7646	Clinical (unspecified phase)
0.567	Remote Similarity	NPD4789	Approved
0.5652	Remote Similarity	NPD4159	Approved
0.5636	Remote Similarity	NPD6703	Approved
0.5636	Remote Similarity	NPD6702	Approved
0.5632	Remote Similarity	NPD890	Clinical (unspecified phase)
0.5632	Remote Similarity	NPD892	Phase 3
0.5632	Remote Similarity	NPD888	Phase 3
0.5632	Remote Similarity	NPD895	Approved
0.5632	Remote Similarity	NPD887	Approved
0.5632	Remote Similarity	NPD894	Approved
0.5632	Remote Similarity	NPD889	Approved
0.5632	Remote Similarity	NPD893	Approved
0.5632	Remote Similarity	NPD891	Phase 3
0.5631	Remote Similarity	NPD4748	Discontinued
0.563	Remote Similarity	NPD6899	Approved
0.563	Remote Similarity	NPD6881	Approved
0.562	Remote Similarity	NPD8130	Phase 1
0.562	Remote Similarity	NPD6650	Approved
0.562	Remote Similarity	NPD6649	Approved
0.5619	Remote Similarity	NPD6695	Phase 3

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