NPASS Compound

Structure

CID282454 OpenBabel06191716092D 33 37 0 0 1 0 0 0 0 0999 V2000 5.3666 -1.3920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6979 -0.5290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0358 -1.3709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0360 -2.3296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7723 -2.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8014 1.4552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8305 0.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3911 -0.4830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7772 0.5707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6018 0.9247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4042 -0.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4037 -3.2379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6403 0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0588 -0.0111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6026 -2.7757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8009 1.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6028 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 -1.8505 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6023 0.0003 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8009 -1.3878 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4042 -1.3881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8014 -1.3881 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2051 -2.7753 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8009 -0.4624 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7849 -0.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2053 -1.8504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6028 -1.8508 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8014 -0.4627 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 3.2034 -0.9241 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6228 -1.8623 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0269 -3.2499 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0665 -1.2554 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 6 28 1 0 0 0 0 9 13 1 0 0 0 0 9 14 1 0 0 0 0 10 16 1 0 0 0 0 11 17 1 0 0 0 0 11 21 1 0 0 0 0 12 15 1 0 0 0 0 12 23 1 0 0 0 0 13 25 1 0 0 0 0 14 30 1 0 0 0 0 15 27 1 0 0 0 0 16 29 1 0 0 0 0 17 28 1 0 0 0 0 18 20 1 0 0 0 0 18 22 1 0 0 0 0 19 10 1 6 0 0 0 19 24 1 0 0 0 0 19 30 1 0 0 0 0 20 24 1 0 0 0 0 20 31 1 6 0 0 0 21 26 1 0 0 0 0 21 27 1 6 0 0 0 22 27 1 6 0 0 0 22 28 1 0 0 0 0 23 26 1 0 0 0 0 23 32 1 6 0 0 0 24 29 1 1 0 0 0 25 33 1 0 0 0 0 27 5 1 6 0 0 0 28 29 1 1 0 0 0 29 7 1 1 0 0 0 30 8 1 6 0 0 0 30 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	460.39
Volume:	511.024
LogP:	5.56
LogD:	5.129
LogS:	-5.32
# Rotatable Bonds:	1
TPSA:	49.69
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.455
Synthetic Accessibility Score:	4.852
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.999
MDCK Permeability:	3.083718183916062e-05
Pgp-inhibitor:	0.362
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.161
30% Bioavailability (F30%):	0.651

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.059
Plasma Protein Binding (PPB):	95.87279510498047%
Volume Distribution (VD):	1.044
Pgp-substrate:	2.9452273845672607%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.5
CYP2C19-inhibitor:	0.069
CYP2C19-substrate:	0.939
CYP2C9-inhibitor:	0.165
CYP2C9-substrate:	0.659
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.796
CYP3A4-inhibitor:	0.255
CYP3A4-substrate:	0.3

ADMET: Excretion

Clearance (CL):	5.298
Half-life (T1/2):	0.223

ADMET: Toxicity

hERG Blockers:	0.094
Human Hepatotoxicity (H-HT):	0.36
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.094
Maximum Recommended Daily Dose:	0.86
Skin Sensitization:	0.378
Carcinogencity:	0.007
Eye Corrosion:	0.696
Eye Irritation:	0.375
Respiratory Toxicity:	0.931

Download Data

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

Natural Product: NPC282454

Natural Product ID:	NPC282454
*Common Name:**	Panaxadiol
IUPAC Name:	(3S,5R,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2R)-2,6,6-trimethyloxan-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,12-diol
Synonyms:	20(R)-Panaxadiol; Panaxadiol
Standard InCHIKey:	PVLHOJXLNBFHDX-XHJPDDKBSA-N
Standard InCHI:	InChI=1S/C30H52O3/c1-25(2)13-9-14-30(8,33-25)19-10-16-29(7)24(19)20(31)18-22-27(5)15-12-23(32)26(3,4)21(27)11-17-28(22,29)6/h19-24,31-32H,9-18H2,1-8H3/t19-,20+,21-,22+,23-,24-,27-,28+,29+,30+/m0/s1
SMILES:	O[C@@H]1C[C@@H]2[C@@]3(C)CC[C@@H](C([C@@H]3CC[C@]2([C@]2([C@H]1[C@H](CC2)[C@@]1(C)CCCC(O1)(C)C)C)C)(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL491655
PubChem CID:	73498
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
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[12880307]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Stems	n.a.	n.a.	PMID[17663584]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[18186611]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Steamed Roots	n.a.	n.a.	PMID[26200131]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21891	Panax notoginseng	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	14
Others	13

Activity Type	# Activity
Cell Line	13
CELL-LINE	1
Individual Protein	7
NON-MOLECULAR	3
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT202	Individual Protein	Protease	Human immunodeficiency virus 1	IC50	>	217100.0	nM	PMID[490529]
NPT1045	Cell Line	U2OS	Homo sapiens	IC50	=	26810.0	nM	PMID[490530]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	37910.0	nM	PMID[490530]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	43130.0	nM	PMID[490530]
NPT1045	Cell Line	U2OS	Homo sapiens	Activity	=	53.35	%	PMID[490530]
NPT1045	Cell Line	U2OS	Homo sapiens	Activity	=	25.73	%	PMID[490530]
NPT65	Cell Line	HepG2	Homo sapiens	Activity	=	68.98	%	PMID[490530]
NPT65	Cell Line	HepG2	Homo sapiens	Activity	=	37.66	%	PMID[490530]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	36.0	%	PMID[490530]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	24.5	%	PMID[490530]
NPT66	Individual Protein	Acetylcholinesterase	Electrophorus electricus	Inhibition	=	7.82	%	PMID[490531]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	52620.0	nM	PMID[490532]
NPT1535	Cell Line	U-87 MG	Homo sapiens	IC50	>	100000.0	nM	PMID[490532]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	44570.0	nM	PMID[490532]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	100000.0	nM	PMID[490532]
NPT5109	Individual Protein	Creatine kinase M	Homo sapiens	Activity	=	7.1	%	PMID[490533]
NPT5109	Individual Protein	Creatine kinase M	Homo sapiens	Activity	=	14.4	%	PMID[490533]
NPT5109	Individual Protein	Creatine kinase M	Homo sapiens	Activity	=	15.4	%	PMID[490533]
NPT211	Individual Protein	Hypoxia-inducible factor 1 alpha	Homo sapiens	IC50	=	9100.0	nM	PMID[490534]
NPT2	Others	Unspecified		IC50	>	217100.0	nM	PMID[490529]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	5610.0	nM	PMID[490530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	18.79	%	PMID[490530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	12.45	%	PMID[490530]
NPT67	Individual Protein	Cholinesterase	Equus caballus	Inhibition	=	12.14	%	PMID[490531]
NPT2	Others	Unspecified		IC50	>	100000.0	nM	PMID[490532]
NPT20904	CELL-LINE	Hep 3B2	Homo sapiens	IC50	=	31700.0	nM	PMID[490534]

☑ 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 NPC282454 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	399
0.1-0.2	4406
0.2-0.3	16544
0.3-0.4	9171
0.4-0.5	4584
0.5-0.6	4164
0.6-0.7	2530
0.7-0.8	723
0.8-0.85	120
0.85-0.9	38
0.9-0.95	11
0.95-1	7

Similarity Score	Similarity Level	Natural Product ID
0.9848	High Similarity	NPC109457
0.9848	High Similarity	NPC157422
0.9848	High Similarity	NPC100586
0.9552	High Similarity	NPC473279
0.9394	High Similarity	NPC472741
0.9275	High Similarity	NPC477508
0.9242	High Similarity	NPC48079
0.9091	High Similarity	NPC142712
0.8986	High Similarity	NPC1340
0.8986	High Similarity	NPC195530
0.8986	High Similarity	NPC127094
0.8986	High Similarity	NPC157777
0.8986	High Similarity	NPC187471
0.8986	High Similarity	NPC470071
0.8986	High Similarity	NPC131506
0.8986	High Similarity	NPC252182
0.8971	High Similarity	NPC129829
0.8971	High Similarity	NPC254037
0.8971	High Similarity	NPC66407
0.8923	High Similarity	NPC114891
0.8841	High Similarity	NPC231945
0.8841	High Similarity	NPC192192
0.8806	High Similarity	NPC44122
0.8769	High Similarity	NPC148174
0.8769	High Similarity	NPC71460
0.8769	High Similarity	NPC218585
0.8714	High Similarity	NPC8004
0.8714	High Similarity	NPC127283
0.8696	High Similarity	NPC241085
0.8696	High Similarity	NPC477820
0.8696	High Similarity	NPC299948
0.8696	High Similarity	NPC470830
0.8696	High Similarity	NPC107919
0.8676	High Similarity	NPC473230
0.8676	High Similarity	NPC475884
0.8657	High Similarity	NPC473276
0.8657	High Similarity	NPC41577
0.8657	High Similarity	NPC474380
0.863	High Similarity	NPC64081
0.863	High Similarity	NPC474574
0.863	High Similarity	NPC476233
0.8611	High Similarity	NPC270306
0.8611	High Similarity	NPC91387
0.8611	High Similarity	NPC231680
0.8592	High Similarity	NPC473238
0.8592	High Similarity	NPC253805
0.8592	High Similarity	NPC472341
0.8571	High Similarity	NPC251201
0.8571	High Similarity	NPC232925
0.8571	High Similarity	NPC63588
0.8514	High Similarity	NPC471769
0.8507	High Similarity	NPC159654
0.8507	High Similarity	NPC167995
0.8507	High Similarity	NPC69149
0.8507	High Similarity	NPC118937
0.8507	High Similarity	NPC281540
0.8493	Intermediate Similarity	NPC470145
0.8472	Intermediate Similarity	NPC304499
0.8472	Intermediate Similarity	NPC10476
0.8472	Intermediate Similarity	NPC192501
0.8472	Intermediate Similarity	NPC228994
0.8451	Intermediate Similarity	NPC478103
0.8421	Intermediate Similarity	NPC73515
0.8406	Intermediate Similarity	NPC63190
0.84	Intermediate Similarity	NPC477282
0.84	Intermediate Similarity	NPC81074
0.84	Intermediate Similarity	NPC220379
0.8382	Intermediate Similarity	NPC260116
0.8382	Intermediate Similarity	NPC80463
0.8378	Intermediate Similarity	NPC133596
0.8378	Intermediate Similarity	NPC11907
0.8356	Intermediate Similarity	NPC196136
0.8356	Intermediate Similarity	NPC317242
0.8356	Intermediate Similarity	NPC243027
0.8356	Intermediate Similarity	NPC158208
0.8356	Intermediate Similarity	NPC3403
0.8333	Intermediate Similarity	NPC153719
0.8333	Intermediate Similarity	NPC470610
0.8312	Intermediate Similarity	NPC296734
0.8308	Intermediate Similarity	NPC476735
0.8289	Intermediate Similarity	NPC7479
0.8289	Intermediate Similarity	NPC257296
0.8289	Intermediate Similarity	NPC248944
0.8289	Intermediate Similarity	NPC16449
0.8267	Intermediate Similarity	NPC471045
0.8243	Intermediate Similarity	NPC14112
0.8243	Intermediate Similarity	NPC163597
0.8243	Intermediate Similarity	NPC86305
0.8228	Intermediate Similarity	NPC290612
0.8219	Intermediate Similarity	NPC48795
0.8169	Intermediate Similarity	NPC99264
0.8158	Intermediate Similarity	NPC476176
0.8154	Intermediate Similarity	NPC236588
0.8154	Intermediate Similarity	NPC135438
0.8133	Intermediate Similarity	NPC212453
0.8133	Intermediate Similarity	NPC105208
0.8133	Intermediate Similarity	NPC475031
0.8133	Intermediate Similarity	NPC185915
0.8133	Intermediate Similarity	NPC192046
0.8133	Intermediate Similarity	NPC128951
0.8133	Intermediate Similarity	NPC477227
0.8133	Intermediate Similarity	NPC23884
0.8133	Intermediate Similarity	NPC302578
0.8116	Intermediate Similarity	NPC243469
0.8116	Intermediate Similarity	NPC472946
0.8116	Intermediate Similarity	NPC475943
0.8116	Intermediate Similarity	NPC190827
0.8108	Intermediate Similarity	NPC195155
0.8108	Intermediate Similarity	NPC104387
0.8108	Intermediate Similarity	NPC178383
0.8108	Intermediate Similarity	NPC174964
0.8108	Intermediate Similarity	NPC240235
0.8108	Intermediate Similarity	NPC231256
0.8108	Intermediate Similarity	NPC212879
0.8108	Intermediate Similarity	NPC97534
0.8088	Intermediate Similarity	NPC292419
0.8088	Intermediate Similarity	NPC290791
0.8082	Intermediate Similarity	NPC232112
0.8077	Intermediate Similarity	NPC202688
0.8077	Intermediate Similarity	NPC60018
0.8077	Intermediate Similarity	NPC154043
0.8077	Intermediate Similarity	NPC475388
0.803	Intermediate Similarity	NPC162685
0.8028	Intermediate Similarity	NPC475893
0.8028	Intermediate Similarity	NPC474756
0.8026	Intermediate Similarity	NPC301707
0.8026	Intermediate Similarity	NPC147993
0.8026	Intermediate Similarity	NPC42853
0.8026	Intermediate Similarity	NPC67657
0.8026	Intermediate Similarity	NPC18857
0.8025	Intermediate Similarity	NPC43912
0.8025	Intermediate Similarity	NPC140446
0.8	Intermediate Similarity	NPC78067
0.8	Intermediate Similarity	NPC273290
0.8	Intermediate Similarity	NPC475742
0.8	Intermediate Similarity	NPC91573
0.8	Intermediate Similarity	NPC278091
0.8	Intermediate Similarity	NPC5767
0.8	Intermediate Similarity	NPC93662
0.8	Intermediate Similarity	NPC232044
0.7975	Intermediate Similarity	NPC470929
0.7975	Intermediate Similarity	NPC470070
0.7975	Intermediate Similarity	NPC477285
0.7975	Intermediate Similarity	NPC111582
0.7973	Intermediate Similarity	NPC478130
0.7973	Intermediate Similarity	NPC25511
0.7973	Intermediate Similarity	NPC62657
0.7973	Intermediate Similarity	NPC475458
0.7973	Intermediate Similarity	NPC192638
0.7949	Intermediate Similarity	NPC58631
0.7945	Intermediate Similarity	NPC156277
0.7945	Intermediate Similarity	NPC111234
0.7945	Intermediate Similarity	NPC320549
0.7945	Intermediate Similarity	NPC151018
0.7945	Intermediate Similarity	NPC58057
0.7941	Intermediate Similarity	NPC185547
0.7941	Intermediate Similarity	NPC95804
0.7922	Intermediate Similarity	NPC287452
0.7922	Intermediate Similarity	NPC80530
0.7922	Intermediate Similarity	NPC273410
0.7922	Intermediate Similarity	NPC155924
0.7922	Intermediate Similarity	NPC49599
0.7922	Intermediate Similarity	NPC49627
0.7917	Intermediate Similarity	NPC470833
0.791	Intermediate Similarity	NPC95958
0.7901	Intermediate Similarity	NPC471240
0.7895	Intermediate Similarity	NPC212241
0.7895	Intermediate Similarity	NPC221420
0.7895	Intermediate Similarity	NPC119355
0.7895	Intermediate Similarity	NPC207010
0.7895	Intermediate Similarity	NPC143133
0.7895	Intermediate Similarity	NPC317913
0.7895	Intermediate Similarity	NPC248830
0.7895	Intermediate Similarity	NPC171658
0.7895	Intermediate Similarity	NPC298168
0.7895	Intermediate Similarity	NPC202540
0.7887	Intermediate Similarity	NPC476928
0.7887	Intermediate Similarity	NPC204233
0.7875	Intermediate Similarity	NPC86238
0.7875	Intermediate Similarity	NPC227260
0.7875	Intermediate Similarity	NPC320824
0.7875	Intermediate Similarity	NPC474996
0.7867	Intermediate Similarity	NPC70982
0.7867	Intermediate Similarity	NPC212733
0.7867	Intermediate Similarity	NPC273366
0.7867	Intermediate Similarity	NPC185536
0.7867	Intermediate Similarity	NPC186851
0.7867	Intermediate Similarity	NPC230704
0.7848	Intermediate Similarity	NPC470611
0.7848	Intermediate Similarity	NPC477286
0.7848	Intermediate Similarity	NPC289486
0.7848	Intermediate Similarity	NPC61107
0.7848	Intermediate Similarity	NPC286719
0.7831	Intermediate Similarity	NPC131466
0.7831	Intermediate Similarity	NPC82955
0.7826	Intermediate Similarity	NPC249078
0.7826	Intermediate Similarity	NPC209686
0.7826	Intermediate Similarity	NPC236099
0.7821	Intermediate Similarity	NPC475679
0.7821	Intermediate Similarity	NPC261616

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 NPC282454 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	403
0.1-0.2	4277
0.2-0.3	3205
0.3-0.4	750
0.4-0.5	196
0.5-0.6	221
0.6-0.7	68
0.7-0.8	27
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8696	High Similarity	NPD4267	Clinical (unspecified phase)
0.831	Intermediate Similarity	NPD4787	Phase 1
0.8289	Intermediate Similarity	NPD6928	Phase 2
0.7945	Intermediate Similarity	NPD4809	Clinical (unspecified phase)
0.7945	Intermediate Similarity	NPD4808	Clinical (unspecified phase)
0.7895	Intermediate Similarity	NPD6116	Phase 1
0.7821	Intermediate Similarity	NPD7525	Registered
0.7763	Intermediate Similarity	NPD6117	Approved
0.7733	Intermediate Similarity	NPD6113	Clinical (unspecified phase)
0.7671	Intermediate Similarity	NPD3699	Clinical (unspecified phase)
0.7671	Intermediate Similarity	NPD3700	Clinical (unspecified phase)
0.7564	Intermediate Similarity	NPD6118	Approved
0.7564	Intermediate Similarity	NPD6114	Approved
0.7564	Intermediate Similarity	NPD6697	Approved
0.7564	Intermediate Similarity	NPD6115	Approved
0.7534	Intermediate Similarity	NPD5361	Clinical (unspecified phase)
0.7534	Intermediate Similarity	NPD5360	Phase 3
0.7403	Intermediate Similarity	NPD3703	Phase 2
0.7333	Intermediate Similarity	NPD4244	Approved
0.7333	Intermediate Similarity	NPD4789	Approved
0.7333	Intermediate Similarity	NPD4245	Approved
0.72	Intermediate Similarity	NPD3698	Phase 2
0.7179	Intermediate Similarity	NPD3702	Approved
0.7159	Intermediate Similarity	NPD8171	Discontinued
0.7143	Intermediate Similarity	NPD7520	Clinical (unspecified phase)
0.7123	Intermediate Similarity	NPD3171	Clinical (unspecified phase)
0.7045	Intermediate Similarity	NPD8034	Phase 2
0.7045	Intermediate Similarity	NPD8035	Phase 2
0.7037	Intermediate Similarity	NPD7645	Phase 2
0.7013	Intermediate Similarity	NPD4758	Discontinued
0.6986	Remote Similarity	NPD371	Approved
0.6962	Remote Similarity	NPD7339	Approved
0.6962	Remote Similarity	NPD6942	Approved
0.6914	Remote Similarity	NPD3671	Phase 1
0.6842	Remote Similarity	NPD6705	Phase 1
0.6813	Remote Similarity	NPD7991	Discontinued
0.6795	Remote Similarity	NPD5777	Approved
0.6747	Remote Similarity	NPD4748	Discontinued
0.6707	Remote Similarity	NPD5364	Discontinued
0.6667	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6625	Remote Similarity	NPD6924	Approved
0.6625	Remote Similarity	NPD6926	Approved
0.6615	Remote Similarity	NPD385	Approved
0.6615	Remote Similarity	NPD384	Approved
0.6582	Remote Similarity	NPD6081	Approved
0.6579	Remote Similarity	NPD4224	Phase 2
0.6556	Remote Similarity	NPD6700	Approved
0.6556	Remote Similarity	NPD6701	Clinical (unspecified phase)
0.6512	Remote Similarity	NPD4788	Approved
0.6484	Remote Similarity	NPD6702	Approved
0.6484	Remote Similarity	NPD6703	Approved
0.6477	Remote Similarity	NPD8308	Discontinued
0.6463	Remote Similarity	NPD6933	Approved
0.6444	Remote Similarity	NPD5328	Approved
0.6437	Remote Similarity	NPD4786	Approved
0.6437	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.642	Remote Similarity	NPD1811	Approved
0.642	Remote Similarity	NPD1810	Approved
0.6413	Remote Similarity	NPD4202	Approved
0.6375	Remote Similarity	NPD4243	Approved
0.6364	Remote Similarity	NPD6920	Discontinued
0.6353	Remote Similarity	NPD7509	Discontinued
0.6322	Remote Similarity	NPD6695	Phase 3
0.6304	Remote Similarity	NPD6079	Approved
0.6292	Remote Similarity	NPD3618	Phase 1
0.625	Remote Similarity	NPD7638	Approved
0.6237	Remote Similarity	NPD6399	Phase 3
0.6222	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.622	Remote Similarity	NPD4785	Approved
0.622	Remote Similarity	NPD4784	Approved
0.6207	Remote Similarity	NPD3667	Approved
0.62	Remote Similarity	NPD7128	Approved
0.62	Remote Similarity	NPD6675	Approved
0.62	Remote Similarity	NPD6402	Approved
0.62	Remote Similarity	NPD5739	Approved
0.6186	Remote Similarity	NPD7639	Approved
0.6186	Remote Similarity	NPD7640	Approved
0.6173	Remote Similarity	NPD7150	Approved
0.6173	Remote Similarity	NPD7151	Approved
0.6173	Remote Similarity	NPD7152	Approved
0.6163	Remote Similarity	NPD6931	Approved
0.6163	Remote Similarity	NPD6930	Phase 2
0.6146	Remote Similarity	NPD7920	Phase 3
0.6146	Remote Similarity	NPD4755	Approved
0.6146	Remote Similarity	NPD7919	Phase 3
0.6125	Remote Similarity	NPD6923	Approved
0.6125	Remote Similarity	NPD6922	Approved
0.6082	Remote Similarity	NPD8088	Phase 1
0.6078	Remote Similarity	NPD6415	Discontinued
0.6078	Remote Similarity	NPD7320	Approved
0.6078	Remote Similarity	NPD6899	Approved
0.6078	Remote Similarity	NPD6881	Approved
0.6061	Remote Similarity	NPD7632	Discontinued
0.6049	Remote Similarity	NPD7143	Approved
0.6049	Remote Similarity	NPD2254	Approved
0.6049	Remote Similarity	NPD2687	Approved
0.6049	Remote Similarity	NPD7144	Approved
0.6049	Remote Similarity	NPD2686	Approved
0.6047	Remote Similarity	NPD6929	Approved
0.6044	Remote Similarity	NPD7524	Approved
0.6044	Remote Similarity	NPD7750	Discontinued
0.602	Remote Similarity	NPD4700	Approved
0.602	Remote Similarity	NPD8418	Phase 2
0.602	Remote Similarity	NPD5286	Approved
0.602	Remote Similarity	NPD5285	Approved
0.602	Remote Similarity	NPD4696	Approved
0.6019	Remote Similarity	NPD6372	Approved
0.6019	Remote Similarity	NPD6373	Approved
0.6019	Remote Similarity	NPD7328	Approved
0.6019	Remote Similarity	NPD7327	Approved
0.6	Remote Similarity	NPD6932	Approved
0.6	Remote Similarity	NPD7748	Approved
0.598	Remote Similarity	NPD5697	Approved
0.598	Remote Similarity	NPD7646	Clinical (unspecified phase)
0.598	Remote Similarity	NPD5701	Approved
0.5979	Remote Similarity	NPD7902	Approved
0.597	Remote Similarity	NPD388	Approved
0.597	Remote Similarity	NPD386	Approved
0.5963	Remote Similarity	NPD7516	Approved
0.5962	Remote Similarity	NPD7102	Approved
0.5962	Remote Similarity	NPD7290	Approved
0.5962	Remote Similarity	NPD6883	Approved
0.596	Remote Similarity	NPD5223	Approved
0.596	Remote Similarity	NPD4159	Approved
0.5957	Remote Similarity	NPD7515	Phase 2
0.5952	Remote Similarity	NPD4190	Phase 3
0.5952	Remote Similarity	NPD5275	Approved
0.5943	Remote Similarity	NPD8133	Approved
0.5922	Remote Similarity	NPD6011	Approved
0.5909	Remote Similarity	NPD8377	Approved
0.5909	Remote Similarity	NPD8294	Approved
0.5909	Remote Similarity	NPD367	Approved
0.5905	Remote Similarity	NPD6650	Approved
0.5905	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.5905	Remote Similarity	NPD6617	Approved
0.5905	Remote Similarity	NPD6847	Approved
0.5905	Remote Similarity	NPD8130	Phase 1
0.5905	Remote Similarity	NPD6649	Approved
0.5905	Remote Similarity	NPD6869	Approved
0.59	Remote Similarity	NPD5211	Phase 2
0.59	Remote Similarity	NPD5226	Approved
0.59	Remote Similarity	NPD4633	Approved
0.59	Remote Similarity	NPD5225	Approved
0.59	Remote Similarity	NPD5224	Approved
0.5889	Remote Similarity	NPD3666	Approved
0.5889	Remote Similarity	NPD3133	Approved
0.5889	Remote Similarity	NPD3665	Phase 1
0.5876	Remote Similarity	NPD5221	Approved
0.5876	Remote Similarity	NPD5222	Approved
0.5876	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.5876	Remote Similarity	NPD4697	Phase 3
0.5865	Remote Similarity	NPD6012	Approved
0.5865	Remote Similarity	NPD6014	Approved
0.5865	Remote Similarity	NPD6013	Approved
0.5862	Remote Similarity	NPD4195	Approved
0.5862	Remote Similarity	NPD6683	Phase 2
0.5856	Remote Similarity	NPD8380	Approved
0.5856	Remote Similarity	NPD8378	Approved
0.5856	Remote Similarity	NPD8379	Approved
0.5856	Remote Similarity	NPD8033	Approved
0.5856	Remote Similarity	NPD8296	Approved
0.5856	Remote Similarity	NPD8335	Approved
0.5849	Remote Similarity	NPD6882	Approved
0.5849	Remote Similarity	NPD8297	Approved
0.5842	Remote Similarity	NPD4754	Approved
0.5842	Remote Similarity	NPD5174	Approved
0.5842	Remote Similarity	NPD5175	Approved
0.5833	Remote Similarity	NPD6940	Discontinued
0.5824	Remote Similarity	NPD6893	Approved
0.5816	Remote Similarity	NPD6084	Phase 2
0.5816	Remote Similarity	NPD6083	Phase 2
0.5816	Remote Similarity	NPD5173	Approved
0.5814	Remote Similarity	NPD6925	Approved
0.5814	Remote Similarity	NPD5776	Phase 2
0.5806	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.5795	Remote Similarity	NPD7514	Phase 3
0.5789	Remote Similarity	NPD7087	Discontinued
0.5784	Remote Similarity	NPD5141	Approved
0.5778	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.5778	Remote Similarity	NPD3669	Approved
0.5769	Remote Similarity	NPD8174	Phase 2
0.5747	Remote Similarity	NPD7145	Approved
0.5747	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5745	Remote Similarity	NPD4753	Phase 2
0.5745	Remote Similarity	NPD6051	Approved
0.5728	Remote Similarity	NPD4768	Approved
0.5728	Remote Similarity	NPD4767	Approved
0.5673	Remote Similarity	NPD6412	Phase 2
0.567	Remote Similarity	NPD7900	Approved
0.567	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD4221	Approved
0.5667	Remote Similarity	NPD4223	Phase 3
0.5663	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD5329	Approved
0.5652	Remote Similarity	NPD7507	Approved
0.5636	Remote Similarity	NPD7115	Discovery
0.5619	Remote Similarity	NPD4729	Approved
0.5619	Remote Similarity	NPD5128	Approved
0.5619	Remote Similarity	NPD5345	Clinical (unspecified phase)

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