NPASS Compound

Structure

NPC82955 OpenBabel07101719522D 46 51 0 0 1 0 0 0 0 0999 V2000 -7.1045 0.6247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6288 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4192 -0.1767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5453 0.2686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3026 2.0624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4286 -0.4920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3026 -1.8607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9246 0.6293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2739 -1.4514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0013 3.0432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0831 -1.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1519 2.5528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2493 -1.3488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8643 -1.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4532 1.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1519 -0.3895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5494 -3.3318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8750 -0.5554 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6038 1.0816 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0013 0.1009 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7000 -2.8414 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3026 1.0816 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8507 2.5528 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6172 -0.7622 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6038 0.1009 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8507 -3.3318 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0013 -2.8414 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0013 -1.8607 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0013 1.0816 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8507 -1.3703 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8507 1.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5966 -0.7109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1519 1.5720 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4532 -0.3895 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3026 0.1009 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9156 -0.3515 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5494 -4.3126 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7544 1.5720 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7000 3.0432 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8507 -4.3126 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1519 -3.3318 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1519 -1.3703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1308 -1.5334 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8507 -0.3895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7000 -1.8607 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 31 1 0 0 0 0 2 31 1 0 0 0 0 3 32 1 0 0 0 0 4 32 1 0 0 0 0 6 34 1 0 0 0 0 9 13 1 0 0 0 0 10 12 1 0 0 0 0 10 23 1 0 0 0 0 11 14 1 0 0 0 0 11 24 1 0 0 0 0 12 33 1 0 0 0 0 13 34 1 0 0 0 0 14 36 1 0 0 0 0 15 19 1 0 0 0 0 15 22 1 0 0 0 0 16 20 1 0 0 0 0 16 35 1 0 0 0 0 17 37 1 0 0 0 0 18 9 1 1 0 0 0 18 25 1 0 0 0 0 18 36 1 0 0 0 0 19 25 1 0 0 0 0 19 38 1 1 0 0 0 20 29 1 0 0 0 0 20 44 1 6 0 0 0 21 17 1 1 0 0 0 21 26 1 0 0 0 0 21 45 1 0 0 0 0 22 33 1 1 0 0 0 22 35 1 0 0 0 0 23 31 1 0 0 0 0 23 39 1 1 0 0 0 24 32 1 6 0 0 0 24 46 1 0 0 0 0 25 34 1 6 0 0 0 26 27 1 0 0 0 0 26 40 1 6 0 0 0 27 28 1 0 0 0 0 27 41 1 1 0 0 0 28 30 1 0 0 0 0 28 42 1 6 0 0 0 29 31 1 0 0 0 0 29 33 1 1 0 0 0 30 44 1 1 0 0 0 30 45 1 0 0 0 0 32 43 1 0 0 0 0 33 5 1 1 0 0 0 34 35 1 1 0 0 0 35 7 1 1 0 0 0 36 8 1 6 0 0 0 36 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	654.43
Volume:	667.775
LogP:	3.391
LogD:	3.87
LogS:	-3.481
# Rotatable Bonds:	5
TPSA:	169.3
# H-Bond Aceptor:	10
# H-Bond Donor:	7
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.219
Synthetic Accessibility Score:	5.624
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:	-5.076
MDCK Permeability:	5.483971835928969e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.057
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.114
30% Bioavailability (F30%):	0.769

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	65.72427368164062%
Volume Distribution (VD):	0.458
Pgp-substrate:	11.299592971801758%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.117
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.775
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.04
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.113
CYP3A4-inhibitor:	0.081
CYP3A4-substrate:	0.16

ADMET: Excretion

Clearance (CL):	1.183
Half-life (T1/2):	0.58

ADMET: Toxicity

hERG Blockers:	0.155
Human Hepatotoxicity (H-HT):	0.213
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.061
Rat Oral Acute Toxicity:	0.34
Maximum Recommended Daily Dose:	0.219
Skin Sensitization:	0.903
Carcinogencity:	0.009
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.978

Download Data

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

Natural Product: NPC82955

Natural Product ID:	NPC82955
*Common Name:**	Pseudo-Ginsenoside Rt
IUPAC Name:	(2R,3R,4S,5S,6R)-2-[[(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-3,12-dihydroxy-17-[(2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-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-6-yl]oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:	(24S)-Pseudo-Ginsenoside Rt4; Pseudo-Ginsenoside Rt
Standard InCHIKey:	PSOUXXNNRFNUAY-ICKHAABJSA-N
Standard InCHI:	InChI=1S/C36H62O10/c1-31(2)23(39)10-12-33(5)22-15-19(38)25-18(36(8)14-11-24(46-36)32(3,4)43)9-13-34(25,6)35(22,7)16-20(29(31)33)44-30-28(42)27(41)26(40)21(17-37)45-30/h18-30,37-43H,9-17H2,1-8H3/t18-,19+,20-,21+,22+,23-,24-,25-,26+,27-,28+,29-,30+,33+,34+,35+,36-/m0/s1
SMILES:	OC[C@H]1O[C@@H](O[C@H]2C[C@@]3(C)[C@]4(C)CC[C@@H]([C@H]4[C@@H](C[C@@H]3[C@@]3([C@@H]2C(C)(C)[C@@H](O)CC3)C)O)[C@]2(C)CC[C@H](O2)C(O)(C)C)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL447942
PubChem CID:	21633074
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
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[11325227]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350149]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28006911]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28202328]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25128	Panax vietnamensis	Species	Araliaceae	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	10

Activity Type	# Activity
Cell Line	11

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell Line	Hepatocyte	Mus musculus	Survival	=	39.4	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Survival	=	57.2	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Survival	=	48.7	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	31.8	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	91.5	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	62.8	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Activity	=	13.6	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Activity	=	39.0	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	Activity	=	26.8	%	PMID[524855]
NPT993	Cell Line	Hepatocyte	Mus musculus	IC50	=	74800.0	nM	PMID[524855]
NPT136	Cell Line	SK-N-SH	Homo sapiens	Activity	=	91.4	%	PMID[524856]

☑ 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 NPC82955 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	511
0.1-0.2	4693
0.2-0.3	13255
0.3-0.4	10751
0.4-0.5	5621
0.5-0.6	3908
0.6-0.7	2495
0.7-0.8	1025
0.8-0.85	207
0.85-0.9	103
0.9-0.95	112
0.95-1	16

Similarity Score	Similarity Level	Natural Product ID
0.9765	High Similarity	NPC210759
0.9765	High Similarity	NPC229801
0.9765	High Similarity	NPC307167
0.9759	High Similarity	NPC140446
0.9759	High Similarity	NPC43912
0.9651	High Similarity	NPC311246
0.9651	High Similarity	NPC167644
0.9647	High Similarity	NPC473542
0.954	High Similarity	NPC175
0.954	High Similarity	NPC45959
0.954	High Similarity	NPC3538
0.954	High Similarity	NPC113500
0.954	High Similarity	NPC477224
0.954	High Similarity	NPC305418
0.954	High Similarity	NPC252253
0.9535	High Similarity	NPC149966
0.9535	High Similarity	NPC5632
0.9529	High Similarity	NPC131466
0.9518	High Similarity	NPC290612
0.9432	High Similarity	NPC473067
0.9432	High Similarity	NPC473065
0.9432	High Similarity	NPC473064
0.9425	High Similarity	NPC149400
0.9425	High Similarity	NPC88962
0.9425	High Similarity	NPC144790
0.9419	High Similarity	NPC279329
0.9412	High Similarity	NPC281004
0.9326	High Similarity	NPC238796
0.9326	High Similarity	NPC142264
0.9326	High Similarity	NPC237071
0.9326	High Similarity	NPC304011
0.9326	High Similarity	NPC139271
0.9326	High Similarity	NPC203434
0.9326	High Similarity	NPC476510
0.9318	High Similarity	NPC253268
0.9318	High Similarity	NPC473851
0.9318	High Similarity	NPC174024
0.9318	High Similarity	NPC291547
0.9318	High Similarity	NPC312678
0.9318	High Similarity	NPC475436
0.9318	High Similarity	NPC473774
0.9318	High Similarity	NPC179859
0.9318	High Similarity	NPC131693
0.9318	High Similarity	NPC24960
0.931	High Similarity	NPC293609
0.931	High Similarity	NPC36372
0.9302	High Similarity	NPC20822
0.9302	High Similarity	NPC102725
0.9302	High Similarity	NPC473472
0.9222	High Similarity	NPC233649
0.9222	High Similarity	NPC477222
0.9222	High Similarity	NPC477223
0.9222	High Similarity	NPC470028
0.9213	High Similarity	NPC474399
0.9205	High Similarity	NPC177834
0.9205	High Similarity	NPC297348
0.9205	High Similarity	NPC141769
0.9205	High Similarity	NPC250393
0.9205	High Similarity	NPC477451
0.9205	High Similarity	NPC325828
0.9205	High Similarity	NPC48339
0.9205	High Similarity	NPC249204
0.9205	High Similarity	NPC277774
0.9205	High Similarity	NPC234352
0.9205	High Similarity	NPC477547
0.9195	High Similarity	NPC65550
0.9195	High Similarity	NPC223143
0.9121	High Similarity	NPC473638
0.9111	High Similarity	NPC121453
0.9101	High Similarity	NPC151214
0.9101	High Similarity	NPC222731
0.9101	High Similarity	NPC309866
0.9101	High Similarity	NPC217205
0.9101	High Similarity	NPC191915
0.9101	High Similarity	NPC264101
0.9101	High Similarity	NPC471464
0.9101	High Similarity	NPC473503
0.9101	High Similarity	NPC291203
0.9101	High Similarity	NPC30687
0.9101	High Similarity	NPC294686
0.9091	High Similarity	NPC473830
0.9091	High Similarity	NPC476668
0.9091	High Similarity	NPC473637
0.9091	High Similarity	NPC204881
0.9091	High Similarity	NPC59006
0.9011	High Similarity	NPC476112
0.9011	High Similarity	NPC475207
0.9011	High Similarity	NPC274200
0.9011	High Similarity	NPC307534
0.9	High Similarity	NPC473610
0.9	High Similarity	NPC469710
0.9	High Similarity	NPC94582
0.9	High Similarity	NPC475351
0.9	High Similarity	NPC19400
0.9	High Similarity	NPC477494
0.9	High Similarity	NPC211354
0.9	High Similarity	NPC206003
0.9	High Similarity	NPC107962
0.9	High Similarity	NPC473727
0.9	High Similarity	NPC57964
0.9	High Similarity	NPC107188
0.9	High Similarity	NPC92196
0.9	High Similarity	NPC6295
0.8989	High Similarity	NPC476669
0.8989	High Similarity	NPC473726
0.8989	High Similarity	NPC172838
0.8989	High Similarity	NPC137004
0.8925	High Similarity	NPC472081
0.8925	High Similarity	NPC477225
0.8925	High Similarity	NPC108227
0.8925	High Similarity	NPC475574
0.8925	High Similarity	NPC476512
0.8913	High Similarity	NPC473616
0.8913	High Similarity	NPC473518
0.8901	High Similarity	NPC103616
0.8901	High Similarity	NPC132080
0.8901	High Similarity	NPC284104
0.8901	High Similarity	NPC184617
0.8901	High Similarity	NPC287483
0.8901	High Similarity	NPC473287
0.8901	High Similarity	NPC30856
0.8901	High Similarity	NPC252056
0.8901	High Similarity	NPC475643
0.8901	High Similarity	NPC128572
0.8901	High Similarity	NPC84111
0.8901	High Similarity	NPC473601
0.8901	High Similarity	NPC116756
0.8901	High Similarity	NPC232037
0.8901	High Similarity	NPC470865
0.8901	High Similarity	NPC475625
0.8901	High Similarity	NPC470866
0.8901	High Similarity	NPC160426
0.8901	High Similarity	NPC98018
0.8901	High Similarity	NPC470864
0.8901	High Similarity	NPC97700
0.8901	High Similarity	NPC472989
0.8901	High Similarity	NPC470863
0.8901	High Similarity	NPC195297
0.8889	High Similarity	NPC475325
0.8864	High Similarity	NPC228059
0.8851	High Similarity	NPC161928
0.8851	High Similarity	NPC472396
0.8851	High Similarity	NPC210658
0.8837	High Similarity	NPC232044
0.8837	High Similarity	NPC273290
0.883	High Similarity	NPC310138
0.883	High Similarity	NPC470029
0.883	High Similarity	NPC114700
0.883	High Similarity	NPC134967
0.8824	High Similarity	NPC470070
0.8817	High Similarity	NPC470030
0.8804	High Similarity	NPC470861
0.8804	High Similarity	NPC51520
0.8804	High Similarity	NPC303069
0.8804	High Similarity	NPC470862
0.8804	High Similarity	NPC232611
0.8804	High Similarity	NPC115165
0.8804	High Similarity	NPC83137
0.8778	High Similarity	NPC224003
0.8778	High Similarity	NPC323231
0.8778	High Similarity	NPC171741
0.8778	High Similarity	NPC18724
0.8778	High Similarity	NPC470623
0.875	High Similarity	NPC128475
0.8737	High Similarity	NPC139181
0.8737	High Similarity	NPC213190
0.8737	High Similarity	NPC97260
0.8737	High Similarity	NPC476837
0.8721	High Similarity	NPC227260
0.871	High Similarity	NPC291548
0.8706	High Similarity	NPC296734
0.8706	High Similarity	NPC470611
0.8696	High Similarity	NPC156377
0.8696	High Similarity	NPC296936
0.8681	High Similarity	NPC148593
0.8681	High Similarity	NPC471373
0.8681	High Similarity	NPC77717
0.8681	High Similarity	NPC267238
0.8681	High Similarity	NPC253611
0.8675	High Similarity	NPC177343
0.8605	High Similarity	NPC241959
0.8602	High Similarity	NPC470591
0.8587	High Similarity	NPC471429
0.8587	High Similarity	NPC106701
0.8587	High Similarity	NPC471425
0.8587	High Similarity	NPC189575
0.8587	High Similarity	NPC471424
0.8587	High Similarity	NPC205129
0.8571	High Similarity	NPC477282
0.8571	High Similarity	NPC81074
0.8554	High Similarity	NPC11907
0.8554	High Similarity	NPC64081
0.8554	High Similarity	NPC133596
0.8554	High Similarity	NPC474574
0.8526	High Similarity	NPC309425
0.8526	High Similarity	NPC472023
0.8526	High Similarity	NPC476839
0.8526	High Similarity	NPC88000
0.8526	High Similarity	NPC476838
0.8526	High Similarity	NPC129372

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 NPC82955 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	499
0.1-0.2	4451
0.2-0.3	2947
0.3-0.4	667
0.4-0.5	306
0.5-0.6	211
0.6-0.7	52
0.7-0.8	14
0.8-0.85	1
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9205	High Similarity	NPD8171	Discontinued
0.8471	Intermediate Similarity	NPD6928	Phase 2
0.8265	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7711	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7449	Intermediate Similarity	NPD7991	Discontinued
0.7387	Intermediate Similarity	NPD8294	Approved
0.7387	Intermediate Similarity	NPD8377	Approved
0.7364	Intermediate Similarity	NPD7328	Approved
0.7364	Intermediate Similarity	NPD7327	Approved
0.7356	Intermediate Similarity	NPD1811	Approved
0.7356	Intermediate Similarity	NPD1810	Approved
0.7321	Intermediate Similarity	NPD8033	Approved
0.7321	Intermediate Similarity	NPD8378	Approved
0.7321	Intermediate Similarity	NPD8335	Approved
0.7321	Intermediate Similarity	NPD8296	Approved
0.7321	Intermediate Similarity	NPD8380	Approved
0.7321	Intermediate Similarity	NPD8379	Approved
0.7315	Intermediate Similarity	NPD8133	Approved
0.7297	Intermediate Similarity	NPD7516	Approved
0.7011	Intermediate Similarity	NPD2686	Approved
0.7011	Intermediate Similarity	NPD2687	Approved
0.7011	Intermediate Similarity	NPD2254	Approved
0.6944	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.6923	Remote Similarity	NPD7507	Approved
0.6875	Remote Similarity	NPD6940	Discontinued
0.6852	Remote Similarity	NPD8174	Phase 2
0.6848	Remote Similarity	NPD6114	Approved
0.6848	Remote Similarity	NPD6697	Approved
0.6848	Remote Similarity	NPD6118	Approved
0.6848	Remote Similarity	NPD6115	Approved
0.6842	Remote Similarity	NPD3669	Approved
0.6842	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6818	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6759	Remote Similarity	NPD6412	Phase 2
0.675	Remote Similarity	NPD7319	Approved
0.6739	Remote Similarity	NPD6116	Phase 1
0.6724	Remote Similarity	NPD7503	Approved
0.6706	Remote Similarity	NPD371	Approved
0.6667	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7736	Approved
0.663	Remote Similarity	NPD6117	Approved
0.6629	Remote Similarity	NPD4787	Phase 1
0.6526	Remote Similarity	NPD7525	Registered
0.6525	Remote Similarity	NPD6370	Approved
0.6446	Remote Similarity	NPD8293	Discontinued
0.6413	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6374	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.6374	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.6356	Remote Similarity	NPD6059	Approved
0.6356	Remote Similarity	NPD6054	Approved
0.6344	Remote Similarity	NPD3703	Phase 2
0.6333	Remote Similarity	NPD8328	Phase 3
0.632	Remote Similarity	NPD8449	Approved
0.6311	Remote Similarity	NPD8034	Phase 2
0.6311	Remote Similarity	NPD8035	Phase 2
0.627	Remote Similarity	NPD8450	Suspended
0.625	Remote Similarity	NPD6686	Approved
0.6167	Remote Similarity	NPD6015	Approved
0.6167	Remote Similarity	NPD6016	Approved
0.6154	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.6148	Remote Similarity	NPD7492	Approved
0.6122	Remote Similarity	NPD1780	Approved
0.6122	Remote Similarity	NPD1779	Approved
0.6116	Remote Similarity	NPD5988	Approved
0.6098	Remote Similarity	NPD6616	Approved
0.6078	Remote Similarity	NPD7524	Approved
0.6071	Remote Similarity	NPD2267	Suspended
0.6066	Remote Similarity	NPD6067	Discontinued
0.6048	Remote Similarity	NPD7078	Approved
0.6044	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.6044	Remote Similarity	NPD5360	Phase 3
0.604	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6	Remote Similarity	NPD1700	Approved
0.6	Remote Similarity	NPD3702	Approved
0.5982	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.5982	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.598	Remote Similarity	NPD8308	Discontinued
0.5977	Remote Similarity	NPD6123	Approved
0.5965	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5963	Remote Similarity	NPD7638	Approved
0.5941	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5918	Remote Similarity	NPD7645	Phase 2
0.5914	Remote Similarity	NPD4244	Approved
0.5914	Remote Similarity	NPD4245	Approved
0.5914	Remote Similarity	NPD4789	Approved
0.5909	Remote Similarity	NPD7639	Approved
0.5909	Remote Similarity	NPD7640	Approved
0.5905	Remote Similarity	NPD6700	Approved
0.5905	Remote Similarity	NPD6701	Clinical (unspecified phase)
0.5904	Remote Similarity	NPD895	Approved
0.5904	Remote Similarity	NPD887	Approved
0.5904	Remote Similarity	NPD889	Approved
0.5904	Remote Similarity	NPD894	Approved
0.5897	Remote Similarity	NPD6882	Approved
0.5897	Remote Similarity	NPD8297	Approved
0.5873	Remote Similarity	NPD6033	Approved
0.5849	Remote Similarity	NPD6702	Approved
0.5849	Remote Similarity	NPD6703	Approved
0.5842	Remote Similarity	NPD6695	Phase 3
0.5839	Remote Similarity	NPD7625	Phase 1
0.5833	Remote Similarity	NPD6009	Approved
0.582	Remote Similarity	NPD6319	Approved
0.5806	Remote Similarity	NPD3698	Phase 2
0.5804	Remote Similarity	NPD7632	Discontinued
0.5783	Remote Similarity	NPD2269	Approved
0.5776	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5772	Remote Similarity	NPD8517	Approved
0.5772	Remote Similarity	NPD8513	Phase 3
0.5772	Remote Similarity	NPD8515	Approved
0.5772	Remote Similarity	NPD8516	Approved
0.5769	Remote Similarity	NPD7750	Discontinued
0.5766	Remote Similarity	NPD8418	Phase 2
0.5714	Remote Similarity	NPD893	Approved
0.5714	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD890	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD892	Phase 3
0.5714	Remote Similarity	NPD891	Phase 3
0.5714	Remote Similarity	NPD4632	Approved
0.5714	Remote Similarity	NPD888	Phase 3
0.569	Remote Similarity	NPD7320	Approved
0.5684	Remote Similarity	NPD5777	Approved
0.5684	Remote Similarity	NPD6081	Approved
0.5684	Remote Similarity	NPD4758	Discontinued
0.567	Remote Similarity	NPD6942	Approved
0.567	Remote Similarity	NPD7339	Approved
0.5663	Remote Similarity	NPD905	Approved
0.5663	Remote Similarity	NPD904	Phase 3
0.5657	Remote Similarity	NPD5364	Discontinued
0.5657	Remote Similarity	NPD3671	Phase 1
0.5652	Remote Similarity	NPD7128	Approved
0.5652	Remote Similarity	NPD6675	Approved
0.5652	Remote Similarity	NPD5739	Approved
0.5652	Remote Similarity	NPD6402	Approved
0.5641	Remote Similarity	NPD6372	Approved
0.5641	Remote Similarity	NPD6373	Approved
0.5612	Remote Similarity	NPD6933	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