NPASS Compound

Structure

NPC78545 OpenBabel07101718242D 32 35 0 0 1 0 0 0 0 0999 V2000 -0.9000 2.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5909 2.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5180 4.8564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5472 2.4190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2382 1.4680 0.0000 C 0 0 0 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1653 4.3212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8781 3.1622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 1.2601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1871 4.1132 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 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 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 -3.4743 5.2722 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 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 -2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 2 0 0 0 0 6 7 1 0 0 0 0 6 16 1 0 0 0 0 7 17 1 0 0 0 0 8 10 1 0 0 0 0 8 19 1 0 0 0 0 9 11 1 0 0 0 0 9 21 1 0 0 0 0 10 27 1 0 0 0 0 11 28 1 0 0 0 0 12 19 1 0 0 0 0 12 23 1 0 0 0 0 13 24 1 0 0 0 0 14 22 1 0 0 0 0 14 25 1 0 0 0 0 15 18 1 0 0 0 0 15 29 1 0 0 0 0 16 18 1 0 0 0 0 17 2 1 1 0 0 0 17 22 1 0 0 0 0 18 3 1 1 0 0 0 19 30 1 6 0 0 0 20 13 1 1 0 0 0 20 21 1 0 0 0 0 20 26 1 0 0 0 0 21 27 1 6 0 0 0 22 28 1 6 0 0 0 23 24 1 0 0 0 0 23 27 1 6 0 0 0 24 31 1 1 0 0 0 25 26 1 0 0 0 0 25 32 1 6 0 0 0 26 28 1 6 0 0 0 27 4 1 6 0 0 0 28 5 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.36
Volume:	491.143
LogP:	4.561
LogD:	4.597
LogS:	-4.277
# Rotatable Bonds:	6
TPSA:	80.92
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.45
Synthetic Accessibility Score:	5.024
Fsp3:	0.929
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.779
MDCK Permeability:	2.026806578214746e-05
Pgp-inhibitor:	0.458
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.015
20% Bioavailability (F20%):	0.658
30% Bioavailability (F30%):	0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.193
Plasma Protein Binding (PPB):	90.36329650878906%
Volume Distribution (VD):	0.799
Pgp-substrate:	4.181326389312744%

ADMET: Metabolism

CYP1A2-inhibitor:	0.067
CYP1A2-substrate:	0.227
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.609
CYP2C9-inhibitor:	0.047
CYP2C9-substrate:	0.097
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.089
CYP3A4-inhibitor:	0.201
CYP3A4-substrate:	0.233

ADMET: Excretion

Clearance (CL):	8.463
Half-life (T1/2):	0.442

ADMET: Toxicity

hERG Blockers:	0.452
Human Hepatotoxicity (H-HT):	0.329
Drug-inuced Liver Injury (DILI):	0.294
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.333
Skin Sensitization:	0.923
Carcinogencity:	0.133
Eye Corrosion:	0.056
Eye Irritation:	0.243
Respiratory Toxicity:	0.917

Download Data

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

Natural Product: NPC78545

Natural Product ID:	NPC78545
*Common Name:**	Certonardosterol D
IUPAC Name:	(3S,5S,6S,8R,9S,10R,13R,14S,15R,17R)-17-[(2R,6S)-7-hydroxy-6-methyl-5-methylideneheptan-2-yl]-10,13-dimethyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,6,15-triol
Synonyms:	Certonardosterol D
Standard InCHIKey:	KZKDLDINCJUKQF-XYIXAQQTSA-N
Standard InCHI:	InChI=1S/C28H48O4/c1-16(18(3)15-29)6-7-17(2)22-14-25(32)26-20-13-24(31)23-12-19(30)8-10-27(23,4)21(20)9-11-28(22,26)5/h17-26,29-32H,1,6-15H2,2-5H3/t17-,18-,19+,20-,21+,22-,23-,24+,25-,26-,27-,28-/m1/s1
SMILES:	OC[C@H](C(=C)CC[C@H]([C@H]1C[C@H]([C@@H]2[C@]1(C)CC[C@H]1[C@H]2C[C@@H]([C@@H]2[C@]1(C)CC[C@@H](C2)O)O)O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517980
PubChem CID:	21629547
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0001110] Tetrahydroxy bile acids, alcohols and derivatives

*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
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444692]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662097]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104487]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497935]

☑ 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
ED50	5
MIC	20

Activity Type	# Activity
Cell Line	5
Organism	20

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	5.3	ug ml-1	PMID[483653]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	8.5	ug ml-1	PMID[483653]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	5.5	ug ml-1	PMID[483653]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	4.8	ug ml-1	PMID[483653]
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	9.6	ug ml-1	PMID[483653]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	25.0	ug.mL-1	PMID[483653]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	25.0	ug.mL-1	PMID[483653]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT4997	Organism	Klebsiella oxytoca	Klebsiella oxytoca	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	>	25.0	ug.mL-1	PMID[483653]
NPT1033	Organism	Enterobacter cloacae	Enterobacter cloacae	MIC	>	25.0	ug.mL-1	PMID[483653]

☑ 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 NPC78545 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	177
0.1-0.2	2105
0.2-0.3	8326
0.3-0.4	15417
0.4-0.5	6150
0.5-0.6	4771
0.6-0.7	4094
0.7-0.8	1395
0.8-0.85	141
0.85-0.9	85
0.9-0.95	29
0.95-1	7

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC71535
0.973	High Similarity	NPC477817
0.973	High Similarity	NPC477819
0.961	High Similarity	NPC232023
0.9487	High Similarity	NPC255882
0.9474	High Similarity	NPC47149
0.9359	High Similarity	NPC110778
0.9342	High Similarity	NPC24504
0.925	High Similarity	NPC121981
0.925	High Similarity	NPC24277
0.9241	High Similarity	NPC127606
0.9241	High Similarity	NPC256567
0.9241	High Similarity	NPC124172
0.9241	High Similarity	NPC475798
0.9211	High Similarity	NPC472499
0.9211	High Similarity	NPC472500
0.9211	High Similarity	NPC472502
0.9211	High Similarity	NPC475
0.9189	High Similarity	NPC472503
0.9189	High Similarity	NPC308440
0.9114	High Similarity	NPC193870
0.9114	High Similarity	NPC141941
0.9114	High Similarity	NPC477818
0.9103	High Similarity	NPC157655
0.9091	High Similarity	NPC476316
0.9079	High Similarity	NPC202540
0.9079	High Similarity	NPC138502
0.9067	High Similarity	NPC3403
0.9012	High Similarity	NPC201273
0.9	High Similarity	NPC209802
0.8987	High Similarity	NPC470614
0.8987	High Similarity	NPC1272
0.8974	High Similarity	NPC475679
0.8961	High Similarity	NPC42853
0.8961	High Similarity	NPC301707
0.8961	High Similarity	NPC31828
0.8947	High Similarity	NPC14112
0.8947	High Similarity	NPC86305
0.8947	High Similarity	NPC38141
0.8919	High Similarity	NPC111234
0.8916	High Similarity	NPC105495
0.8875	High Similarity	NPC216420
0.8875	High Similarity	NPC211135
0.8875	High Similarity	NPC85095
0.8846	High Similarity	NPC116119
0.8846	High Similarity	NPC472742
0.8846	High Similarity	NPC475727
0.8846	High Similarity	NPC49599
0.8846	High Similarity	NPC80297
0.8846	High Similarity	NPC49627
0.8846	High Similarity	NPC5604
0.8831	High Similarity	NPC260301
0.8831	High Similarity	NPC307336
0.8816	High Similarity	NPC212879
0.8816	High Similarity	NPC240235
0.8816	High Similarity	NPC230704
0.8816	High Similarity	NPC185536
0.8816	High Similarity	NPC178383
0.8816	High Similarity	NPC103822
0.8816	High Similarity	NPC104387
0.8816	High Similarity	NPC70982
0.8816	High Similarity	NPC231256
0.8795	High Similarity	NPC475664
0.8795	High Similarity	NPC470542
0.8784	High Similarity	NPC63588
0.8784	High Similarity	NPC251201
0.8784	High Similarity	NPC45296
0.8784	High Similarity	NPC232925
0.878	High Similarity	NPC6605
0.878	High Similarity	NPC139724
0.8734	High Similarity	NPC26117
0.8734	High Similarity	NPC102253
0.8734	High Similarity	NPC236237
0.8734	High Similarity	NPC322313
0.8718	High Similarity	NPC472501
0.8718	High Similarity	NPC167037
0.8718	High Similarity	NPC244385
0.8718	High Similarity	NPC6978
0.8718	High Similarity	NPC138621
0.8701	High Similarity	NPC91573
0.8701	High Similarity	NPC78067
0.8701	High Similarity	NPC93662
0.8701	High Similarity	NPC278091
0.8684	High Similarity	NPC196358
0.8684	High Similarity	NPC192638
0.8684	High Similarity	NPC62657
0.8684	High Similarity	NPC25511
0.8684	High Similarity	NPC145552
0.8684	High Similarity	NPC5046
0.8684	High Similarity	NPC49168
0.8684	High Similarity	NPC254509
0.8675	High Similarity	NPC474657
0.8675	High Similarity	NPC186145
0.8649	High Similarity	NPC477820
0.8642	High Similarity	NPC470929
0.8608	High Similarity	NPC80530
0.8608	High Similarity	NPC472463
0.8608	High Similarity	NPC1319
0.8608	High Similarity	NPC273410
0.859	High Similarity	NPC248830
0.859	High Similarity	NPC119355
0.859	High Similarity	NPC331618
0.859	High Similarity	NPC212241
0.859	High Similarity	NPC257191
0.8588	High Similarity	NPC473956
0.8588	High Similarity	NPC475751
0.8571	High Similarity	NPC160304
0.8571	High Similarity	NPC200243
0.8553	High Similarity	NPC195489
0.8553	High Similarity	NPC472506
0.8553	High Similarity	NPC470610
0.8537	High Similarity	NPC86238
0.8519	High Similarity	NPC248886
0.8481	Intermediate Similarity	NPC87604
0.8481	Intermediate Similarity	NPC285761
0.8481	Intermediate Similarity	NPC477522
0.8481	Intermediate Similarity	NPC102708
0.8481	Intermediate Similarity	NPC472342
0.8471	Intermediate Similarity	NPC109744
0.8462	Intermediate Similarity	NPC237460
0.8452	Intermediate Similarity	NPC271967
0.8442	Intermediate Similarity	NPC304499
0.8442	Intermediate Similarity	NPC476736
0.8442	Intermediate Similarity	NPC48795
0.8421	Intermediate Similarity	NPC164045
0.8415	Intermediate Similarity	NPC113978
0.8415	Intermediate Similarity	NPC207013
0.84	Intermediate Similarity	NPC66407
0.8395	Intermediate Similarity	NPC470383
0.8391	Intermediate Similarity	NPC26046
0.8372	Intermediate Similarity	NPC194485
0.8372	Intermediate Similarity	NPC53890
0.8372	Intermediate Similarity	NPC219937
0.8372	Intermediate Similarity	NPC123252
0.8353	Intermediate Similarity	NPC2158
0.8333	Intermediate Similarity	NPC261266
0.8333	Intermediate Similarity	NPC152808
0.8333	Intermediate Similarity	NPC6391
0.8333	Intermediate Similarity	NPC317242
0.8333	Intermediate Similarity	NPC293287
0.8315	Intermediate Similarity	NPC304899
0.8315	Intermediate Similarity	NPC253115
0.8313	Intermediate Similarity	NPC299963
0.8313	Intermediate Similarity	NPC242016
0.8313	Intermediate Similarity	NPC474493
0.8312	Intermediate Similarity	NPC153719
0.8295	Intermediate Similarity	NPC3359
0.8293	Intermediate Similarity	NPC201852
0.8293	Intermediate Similarity	NPC477599
0.8293	Intermediate Similarity	NPC472504
0.8276	Intermediate Similarity	NPC130840
0.8272	Intermediate Similarity	NPC13554
0.8256	Intermediate Similarity	NPC74258
0.825	Intermediate Similarity	NPC85346
0.825	Intermediate Similarity	NPC275910
0.825	Intermediate Similarity	NPC302041
0.825	Intermediate Similarity	NPC65897
0.8243	Intermediate Similarity	NPC44122
0.8235	Intermediate Similarity	NPC477600
0.8228	Intermediate Similarity	NPC189883
0.8228	Intermediate Similarity	NPC73875
0.8228	Intermediate Similarity	NPC107059
0.8228	Intermediate Similarity	NPC163597
0.8228	Intermediate Similarity	NPC240604
0.8228	Intermediate Similarity	NPC321381
0.8228	Intermediate Similarity	NPC321016
0.8228	Intermediate Similarity	NPC300324
0.8228	Intermediate Similarity	NPC96319
0.8222	Intermediate Similarity	NPC190554
0.8214	Intermediate Similarity	NPC318390
0.8182	Intermediate Similarity	NPC470071
0.8182	Intermediate Similarity	NPC252182
0.8182	Intermediate Similarity	NPC187471
0.8182	Intermediate Similarity	NPC1340
0.8182	Intermediate Similarity	NPC127094
0.8171	Intermediate Similarity	NPC23852
0.8171	Intermediate Similarity	NPC209620
0.8171	Intermediate Similarity	NPC474531
0.8161	Intermediate Similarity	NPC107189
0.8161	Intermediate Similarity	NPC10274
0.8161	Intermediate Similarity	NPC100313
0.814	Intermediate Similarity	NPC473436
0.814	Intermediate Similarity	NPC471952
0.814	Intermediate Similarity	NPC67872
0.814	Intermediate Similarity	NPC474668
0.8133	Intermediate Similarity	NPC253303
0.8133	Intermediate Similarity	NPC269077
0.8125	Intermediate Similarity	NPC471798
0.8125	Intermediate Similarity	NPC155986
0.8125	Intermediate Similarity	NPC302578
0.8125	Intermediate Similarity	NPC214570
0.8125	Intermediate Similarity	NPC192046
0.8125	Intermediate Similarity	NPC128951
0.8125	Intermediate Similarity	NPC318495
0.8125	Intermediate Similarity	NPC185915
0.8125	Intermediate Similarity	NPC198968
0.8125	Intermediate Similarity	NPC477227
0.8125	Intermediate Similarity	NPC105208
0.8118	Intermediate Similarity	NPC71520
0.8118	Intermediate Similarity	NPC145245

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 NPC78545 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	157
0.1-0.2	2430
0.2-0.3	4335
0.3-0.4	1558
0.4-0.5	252
0.5-0.6	163
0.6-0.7	185
0.7-0.8	68
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8734	High Similarity	NPD7525	Registered
0.8228	Intermediate Similarity	NPD3701	Clinical (unspecified phase)
0.8101	Intermediate Similarity	NPD6942	Approved
0.8101	Intermediate Similarity	NPD7339	Approved
0.7816	Intermediate Similarity	NPD4751	Clinical (unspecified phase)
0.7791	Intermediate Similarity	NPD7520	Clinical (unspecified phase)
0.7692	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7619	Intermediate Similarity	NPD4748	Discontinued
0.7595	Intermediate Similarity	NPD4787	Phase 1
0.7558	Intermediate Similarity	NPD4788	Approved
0.7531	Intermediate Similarity	NPD4784	Approved
0.7531	Intermediate Similarity	NPD4785	Approved
0.7531	Intermediate Similarity	NPD6924	Approved
0.7531	Intermediate Similarity	NPD6926	Approved
0.75	Intermediate Similarity	NPD4243	Approved
0.75	Intermediate Similarity	NPD7645	Phase 2
0.75	Intermediate Similarity	NPD6929	Approved
0.7473	Intermediate Similarity	NPD8035	Phase 2
0.7473	Intermediate Similarity	NPD8034	Phase 2
0.7471	Intermediate Similarity	NPD7338	Clinical (unspecified phase)
0.7471	Intermediate Similarity	NPD4786	Approved
0.7412	Intermediate Similarity	NPD6930	Phase 2
0.7412	Intermediate Similarity	NPD6931	Approved
0.7412	Intermediate Similarity	NPD6928	Phase 2
0.7391	Intermediate Similarity	NPD4202	Approved
0.7381	Intermediate Similarity	NPD6114	Approved
0.7381	Intermediate Similarity	NPD6115	Approved
0.7381	Intermediate Similarity	NPD6118	Approved
0.7381	Intermediate Similarity	NPD6697	Approved
0.7368	Intermediate Similarity	NPD7638	Approved
0.7356	Intermediate Similarity	NPD6695	Phase 3
0.7349	Intermediate Similarity	NPD6933	Approved
0.7292	Intermediate Similarity	NPD7639	Approved
0.7292	Intermediate Similarity	NPD7640	Approved
0.7284	Intermediate Similarity	NPD7150	Approved
0.7284	Intermediate Similarity	NPD7151	Approved
0.7284	Intermediate Similarity	NPD7152	Approved
0.7263	Intermediate Similarity	NPD4755	Approved
0.7262	Intermediate Similarity	NPD5776	Phase 2
0.7262	Intermediate Similarity	NPD6932	Approved
0.7262	Intermediate Similarity	NPD6925	Approved
0.7262	Intermediate Similarity	NPD6116	Phase 1
0.7253	Intermediate Similarity	NPD5328	Approved
0.725	Intermediate Similarity	NPD6923	Approved
0.725	Intermediate Similarity	NPD6922	Approved
0.7241	Intermediate Similarity	NPD3667	Approved
0.7209	Intermediate Similarity	NPD7509	Discontinued
0.7176	Intermediate Similarity	NPD7145	Approved
0.716	Intermediate Similarity	NPD7144	Approved
0.716	Intermediate Similarity	NPD7143	Approved
0.7143	Intermediate Similarity	NPD6117	Approved
0.7113	Intermediate Similarity	NPD4700	Approved
0.7113	Intermediate Similarity	NPD5285	Approved
0.7113	Intermediate Similarity	NPD4696	Approved
0.7113	Intermediate Similarity	NPD5286	Approved
0.7111	Intermediate Similarity	NPD3618	Phase 1
0.7097	Intermediate Similarity	NPD6079	Approved
0.7093	Intermediate Similarity	NPD6683	Phase 2
0.7079	Intermediate Similarity	NPD3133	Approved
0.7079	Intermediate Similarity	NPD3666	Approved
0.7079	Intermediate Similarity	NPD3665	Phase 1
0.7073	Intermediate Similarity	NPD4809	Clinical (unspecified phase)
0.7073	Intermediate Similarity	NPD4808	Clinical (unspecified phase)
0.7041	Intermediate Similarity	NPD5223	Approved
0.7033	Intermediate Similarity	NPD7524	Approved
0.7033	Intermediate Similarity	NPD7750	Discontinued
0.7024	Intermediate Similarity	NPD4190	Phase 3
0.7024	Intermediate Similarity	NPD3703	Phase 2
0.7024	Intermediate Similarity	NPD5275	Approved
0.7021	Intermediate Similarity	NPD6399	Phase 3
0.7011	Intermediate Similarity	NPD7514	Phase 3
0.7	Intermediate Similarity	NPD6893	Approved
0.697	Remote Similarity	NPD5225	Approved
0.697	Remote Similarity	NPD4633	Approved
0.697	Remote Similarity	NPD5226	Approved
0.697	Remote Similarity	NPD5224	Approved
0.697	Remote Similarity	NPD5211	Phase 2
0.6951	Remote Similarity	NPD4244	Approved
0.6951	Remote Similarity	NPD4245	Approved
0.6932	Remote Similarity	NPD6902	Approved
0.6931	Remote Similarity	NPD6675	Approved
0.6931	Remote Similarity	NPD7128	Approved
0.6931	Remote Similarity	NPD6402	Approved
0.6931	Remote Similarity	NPD5739	Approved
0.6905	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.69	Remote Similarity	NPD5174	Approved
0.69	Remote Similarity	NPD4754	Approved
0.69	Remote Similarity	NPD5175	Approved
0.6897	Remote Similarity	NPD4195	Approved
0.6882	Remote Similarity	NPD4753	Phase 2
0.6832	Remote Similarity	NPD5141	Approved
0.6829	Remote Similarity	NPD3698	Phase 2
0.6829	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.6829	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.6827	Remote Similarity	NPD4634	Approved
0.6818	Remote Similarity	NPD7332	Phase 2
0.6804	Remote Similarity	NPD5221	Approved
0.6804	Remote Similarity	NPD4697	Phase 3
0.6804	Remote Similarity	NPD5222	Approved
0.6804	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.68	Remote Similarity	NPD7632	Discontinued
0.6796	Remote Similarity	NPD7320	Approved
0.6796	Remote Similarity	NPD6881	Approved
0.6796	Remote Similarity	NPD6899	Approved
0.6765	Remote Similarity	NPD4767	Approved
0.6765	Remote Similarity	NPD4768	Approved
0.6742	Remote Similarity	NPD6898	Phase 1
0.6737	Remote Similarity	NPD7515	Phase 2
0.6737	Remote Similarity	NPD7087	Discontinued
0.6735	Remote Similarity	NPD5173	Approved
0.6731	Remote Similarity	NPD6372	Approved
0.6731	Remote Similarity	NPD6373	Approved
0.6703	Remote Similarity	NPD3668	Phase 3
0.6699	Remote Similarity	NPD5697	Approved
0.6699	Remote Similarity	NPD5701	Approved
0.6697	Remote Similarity	NPD7328	Approved
0.6697	Remote Similarity	NPD7327	Approved
0.6667	Remote Similarity	NPD7290	Approved
0.6667	Remote Similarity	NPD4223	Phase 3
0.6667	Remote Similarity	NPD6883	Approved
0.6667	Remote Similarity	NPD4221	Approved
0.6667	Remote Similarity	NPD7102	Approved
0.6667	Remote Similarity	NPD8171	Discontinued
0.6667	Remote Similarity	NPD8033	Approved
0.6636	Remote Similarity	NPD4632	Approved
0.6636	Remote Similarity	NPD7516	Approved
0.6635	Remote Similarity	NPD4729	Approved
0.6635	Remote Similarity	NPD4730	Approved
0.6635	Remote Similarity	NPD5128	Approved
0.6635	Remote Similarity	NPD6011	Approved
0.663	Remote Similarity	NPD5329	Approved
0.6604	Remote Similarity	NPD6847	Approved
0.6604	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6604	Remote Similarity	NPD6650	Approved
0.6604	Remote Similarity	NPD6869	Approved
0.6604	Remote Similarity	NPD6617	Approved
0.6604	Remote Similarity	NPD8130	Phase 1
0.6604	Remote Similarity	NPD6649	Approved
0.6602	Remote Similarity	NPD6008	Approved
0.6591	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.6577	Remote Similarity	NPD8294	Approved
0.6577	Remote Similarity	NPD8377	Approved
0.6571	Remote Similarity	NPD6013	Approved
0.6571	Remote Similarity	NPD6012	Approved
0.6571	Remote Similarity	NPD6014	Approved
0.6566	Remote Similarity	NPD6083	Phase 2
0.6566	Remote Similarity	NPD6084	Phase 2
0.6548	Remote Similarity	NPD4789	Approved
0.6542	Remote Similarity	NPD8297	Approved
0.6542	Remote Similarity	NPD6882	Approved
0.6538	Remote Similarity	NPD6412	Phase 2
0.6531	Remote Similarity	NPD4629	Approved
0.6531	Remote Similarity	NPD5210	Approved
0.6526	Remote Similarity	NPD6051	Approved
0.6522	Remote Similarity	NPD4197	Approved
0.6518	Remote Similarity	NPD8379	Approved
0.6518	Remote Similarity	NPD8380	Approved
0.6518	Remote Similarity	NPD8296	Approved
0.6518	Remote Similarity	NPD8335	Approved
0.6518	Remote Similarity	NPD8378	Approved
0.6509	Remote Similarity	NPD5249	Phase 3
0.6509	Remote Similarity	NPD5250	Approved
0.6509	Remote Similarity	NPD5169	Approved
0.6509	Remote Similarity	NPD5251	Approved
0.6509	Remote Similarity	NPD5134	Clinical (unspecified phase)
0.6509	Remote Similarity	NPD5247	Approved
0.6509	Remote Similarity	NPD5135	Approved
0.6509	Remote Similarity	NPD5248	Approved
0.6506	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.6506	Remote Similarity	NPD5360	Phase 3
0.6481	Remote Similarity	NPD8133	Approved
0.6458	Remote Similarity	NPD6700	Approved
0.6458	Remote Similarity	NPD6701	Clinical (unspecified phase)
0.6455	Remote Similarity	NPD6009	Approved
0.6449	Remote Similarity	NPD5215	Approved
0.6449	Remote Similarity	NPD5217	Approved
0.6449	Remote Similarity	NPD5216	Approved
0.6449	Remote Similarity	NPD5127	Approved
0.6437	Remote Similarity	NPD8264	Approved
0.6429	Remote Similarity	NPD6054	Approved
0.6429	Remote Similarity	NPD7748	Approved
0.6429	Remote Similarity	NPD6059	Approved
0.6421	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.64	Remote Similarity	NPD7902	Approved
0.6392	Remote Similarity	NPD7637	Suspended
0.6392	Remote Similarity	NPD6702	Approved
0.6392	Remote Similarity	NPD6703	Approved
0.6383	Remote Similarity	NPD6684	Approved
0.6383	Remote Similarity	NPD7334	Approved
0.6383	Remote Similarity	NPD7146	Approved
0.6383	Remote Similarity	NPD4693	Phase 3
0.6383	Remote Similarity	NPD4689	Approved
0.6383	Remote Similarity	NPD4690	Approved
0.6383	Remote Similarity	NPD5279	Phase 3
0.6383	Remote Similarity	NPD7521	Approved
0.6383	Remote Similarity	NPD5205	Approved
0.6383	Remote Similarity	NPD4138	Approved
0.6383	Remote Similarity	NPD6409	Approved
0.6383	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6383	Remote Similarity	NPD4688	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