NPASS Compound

Structure

CID54123 OpenBabel06191715392D 21 24 0 0 1 0 0 0 0 0999 V2000 2.5073 -0.4461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6722 -2.8938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8364 -2.4116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6700 -0.9648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6703 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1778 -1.4457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6714 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3425 -0.9634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8356 0.4827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3431 -2.8933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5078 -2.4111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1781 -2.4106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8361 -1.4466 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0003 -0.9644 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6717 -0.9639 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8358 0.4822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5075 -1.4461 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0443 -2.9102 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8364 1.4822 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3 4 1 0 0 0 0 3 12 1 0 0 0 0 5 6 1 0 0 0 0 5 15 1 0 0 0 0 6 17 1 0 0 0 0 7 9 2 0 0 0 0 7 13 1 0 0 0 0 8 10 1 0 0 0 0 8 16 1 0 0 0 0 9 18 1 0 0 0 0 10 19 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 12 18 1 0 0 0 0 13 20 2 0 0 0 0 14 4 1 1 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 15 19 1 6 0 0 0 16 18 1 6 0 0 0 17 19 1 0 0 0 0 17 21 2 0 0 0 0 18 1 1 6 0 0 0 19 2 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	284.18
Volume:	309.989
LogP:	3.088
LogD:	3.085
LogS:	-3.868
# Rotatable Bonds:	0
TPSA:	34.14
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.677
Synthetic Accessibility Score:	3.951
Fsp3:	0.684
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.693
MDCK Permeability:	2.9728738809353672e-05
Pgp-inhibitor:	0.976
Pgp-substrate:	0.015
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.06
30% Bioavailability (F30%):	0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.159
Plasma Protein Binding (PPB):	92.09941864013672%
Volume Distribution (VD):	1.302
Pgp-substrate:	5.074425220489502%

ADMET: Metabolism

CYP1A2-inhibitor:	0.27
CYP1A2-substrate:	0.561
CYP2C19-inhibitor:	0.254
CYP2C19-substrate:	0.776
CYP2C9-inhibitor:	0.183
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.614
CYP2D6-substrate:	0.028
CYP3A4-inhibitor:	0.889
CYP3A4-substrate:	0.902

ADMET: Excretion

Clearance (CL):	18.356
Half-life (T1/2):	0.848

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.635
Drug-inuced Liver Injury (DILI):	0.048
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.785
Maximum Recommended Daily Dose:	0.888
Skin Sensitization:	0.937
Carcinogencity:	0.887
Eye Corrosion:	0.251
Eye Irritation:	0.239
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC54123

Natural Product ID:	NPC54123
*Common Name:**	Androstenedone
IUPAC Name:	(8R,9S,10R,13S,14S)-10,13-dimethyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthrene-3,17-dione
Synonyms:
Standard InCHIKey:	LUJVUUWNAPIQQI-QAGGRKNESA-N
Standard InCHI:	InChI=1S/C19H24O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h7,9,11,14-16H,3-6,8,10H2,1-2H3/t14-,15-,16-,18-,19-/m0/s1
SMILES:	C[C@]12C=CC(=O)C=C1CC[C@H]1[C@@H]3CCC(=O)[C@@]3(C)CC[C@H]21
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1078534
PubChem CID:	13472
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003568] Androstane steroids [CHEMONTID:0001467] Androgens 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
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	root	n.a.	PMID[16078700]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23848163]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13608	Plumbago zeylanica	Species	Plumbaginaceae	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	2
Ki	6
Others	13
Potency	5

Activity Type	# Activity
Individual Protein	20
Organism	4
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	320.0	nM	PMID[542488]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	IC50	=	300.0	nM	PMID[542489]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Km	=	20.0	nM	PMID[542489]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	IC50	=	530.0	nM	PMID[542490]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	43.0	nM	PMID[542490]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	952.0	nM	PMID[542490]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	K inact	=	0.059	min-1	PMID[542490]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	260.0	nM	PMID[542491]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	120.0	nM	PMID[542491]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Km	=	760.0	nM	PMID[542491]
NPT135	Individual Protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	56234.1	nM	PMID[542494]
NPT101	Individual Protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency	n.a.	10000.0	nM	PMID[542494]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	29092.9	nM	PMID[542494]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	16360.1	nM	PMID[542494]
NPT446	Individual Protein	Rap guanine nucleotide exchange factor 3	Homo sapiens	Potency	n.a.	125892.5	nM	PMID[542494]
NPT441	Individual Protein	Cytochrome P450 19A1	Homo sapiens	Ki	=	260.0	nM	PMID[542496]
NPT896	Individual Protein	Constitutive androstane receptor	Mus musculus	Remaining activity	=	89.0	%	PMID[542487]
NPT27	Others	Unspecified		T1/2	=	0.2117	hr	PMID[542488]
NPT27	Others	Unspecified		Limiting t1/2	=	12.6	min	PMID[542491]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	Activity	=	14.4	uM (g of spores)-1	PMID[542492]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	Activity	=	22.2	uM (g of spores)-1	PMID[542492]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	Activity	=	16.1	uM (g of spores)-1	PMID[542492]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	Activity	=	15.8	uM (g of spores)-1	PMID[542492]
NPT900	Individual Protein	3-keto-steroid reductase	Homo sapiens	Inhibition	=	21.3	%	PMID[542493]
NPT73	Individual Protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	128.1	%	PMID[542495]
NPT72	Individual Protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	103.97	%	PMID[542495]

☑ 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 NPC54123 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	172
0.1-0.2	1803
0.2-0.3	10135
0.3-0.4	14387
0.4-0.5	7812
0.5-0.6	5500
0.6-0.7	2289
0.7-0.8	489
0.8-0.85	59
0.85-0.9	19
0.9-0.95	18
0.95-1	14

Similarity Score	Similarity Level	Natural Product ID
0.9848	High Similarity	NPC251929
0.9848	High Similarity	NPC2634
0.9848	High Similarity	NPC265782
0.9697	High Similarity	NPC139397
0.9559	High Similarity	NPC251705
0.9559	High Similarity	NPC303613
0.9559	High Similarity	NPC474228
0.9552	High Similarity	NPC260040
0.9552	High Similarity	NPC307176
0.9429	High Similarity	NPC69408
0.942	High Similarity	NPC309852
0.9412	High Similarity	NPC115023
0.9412	High Similarity	NPC234707
0.9412	High Similarity	NPC305501
0.9286	High Similarity	NPC293803
0.9275	High Similarity	NPC470045
0.9275	High Similarity	NPC470044
0.9265	High Similarity	NPC35734
0.9265	High Similarity	NPC159577
0.9265	High Similarity	NPC282593
0.9254	High Similarity	NPC260474
0.9254	High Similarity	NPC188292
0.9242	High Similarity	NPC323005
0.9143	High Similarity	NPC329866
0.9143	High Similarity	NPC255021
0.9143	High Similarity	NPC474796
0.9143	High Similarity	NPC474797
0.9118	High Similarity	NPC182815
0.9014	High Similarity	NPC255650
0.9014	High Similarity	NPC473171
0.8971	High Similarity	NPC20610
0.8971	High Similarity	NPC87141
0.8955	High Similarity	NPC92327
0.8939	High Similarity	NPC469662
0.8939	High Similarity	NPC212210
0.8919	High Similarity	NPC474509
0.8889	High Similarity	NPC469793
0.8889	High Similarity	NPC469796
0.8857	High Similarity	NPC5701
0.8857	High Similarity	NPC470078
0.8841	High Similarity	NPC256846
0.8824	High Similarity	NPC176107
0.8806	High Similarity	NPC251118
0.8788	High Similarity	NPC202118
0.8788	High Similarity	NPC197238
0.8714	High Similarity	NPC40574
0.8696	High Similarity	NPC310992
0.8592	High Similarity	NPC190035
0.8592	High Similarity	NPC225467
0.8592	High Similarity	NPC181204
0.8551	High Similarity	NPC475523
0.8533	High Similarity	NPC90965
0.8533	High Similarity	NPC170793
0.8507	High Similarity	NPC165695
0.8507	High Similarity	NPC288253
0.8485	Intermediate Similarity	NPC127582
0.8451	Intermediate Similarity	NPC477856
0.8451	Intermediate Similarity	NPC214770
0.8442	Intermediate Similarity	NPC472239
0.8429	Intermediate Similarity	NPC155198
0.8406	Intermediate Similarity	NPC176171
0.84	Intermediate Similarity	NPC470052
0.84	Intermediate Similarity	NPC82635
0.8382	Intermediate Similarity	NPC475124
0.8382	Intermediate Similarity	NPC285371
0.8378	Intermediate Similarity	NPC1254
0.8378	Intermediate Similarity	NPC474463
0.8358	Intermediate Similarity	NPC213152
0.8354	Intermediate Similarity	NPC29447
0.8333	Intermediate Similarity	NPC472304
0.8333	Intermediate Similarity	NPC223187
0.8333	Intermediate Similarity	NPC276764
0.8333	Intermediate Similarity	NPC259261
0.831	Intermediate Similarity	NPC286814
0.831	Intermediate Similarity	NPC477857
0.8267	Intermediate Similarity	NPC91665
0.8243	Intermediate Similarity	NPC476346
0.8235	Intermediate Similarity	NPC32285
0.8209	Intermediate Similarity	NPC25853
0.8205	Intermediate Similarity	NPC100297
0.8205	Intermediate Similarity	NPC472867
0.8205	Intermediate Similarity	NPC193347
0.8205	Intermediate Similarity	NPC320514
0.8205	Intermediate Similarity	NPC469806
0.8205	Intermediate Similarity	NPC469804
0.8205	Intermediate Similarity	NPC3511
0.8205	Intermediate Similarity	NPC142253
0.8205	Intermediate Similarity	NPC469805
0.8205	Intermediate Similarity	NPC469799
0.8182	Intermediate Similarity	NPC476809
0.8182	Intermediate Similarity	NPC60772
0.8182	Intermediate Similarity	NPC266295
0.8182	Intermediate Similarity	NPC311852
0.8182	Intermediate Similarity	NPC472478
0.8182	Intermediate Similarity	NPC469798
0.8182	Intermediate Similarity	NPC469797
0.8182	Intermediate Similarity	NPC94991
0.8182	Intermediate Similarity	NPC56905
0.8182	Intermediate Similarity	NPC27610
0.8169	Intermediate Similarity	NPC82477
0.8169	Intermediate Similarity	NPC142754
0.8169	Intermediate Similarity	NPC296697
0.8169	Intermediate Similarity	NPC39157
0.8158	Intermediate Similarity	NPC115515
0.8158	Intermediate Similarity	NPC469996
0.8148	Intermediate Similarity	NPC93778
0.8108	Intermediate Similarity	NPC211641
0.8108	Intermediate Similarity	NPC219232
0.8108	Intermediate Similarity	NPC128346
0.8101	Intermediate Similarity	NPC279639
0.8101	Intermediate Similarity	NPC474976
0.8101	Intermediate Similarity	NPC474790
0.8101	Intermediate Similarity	NPC3856
0.8088	Intermediate Similarity	NPC60565
0.8082	Intermediate Similarity	NPC474562
0.8052	Intermediate Similarity	NPC190211
0.803	Intermediate Similarity	NPC115385
0.8028	Intermediate Similarity	NPC290350
0.8028	Intermediate Similarity	NPC20181
0.8028	Intermediate Similarity	NPC220210
0.8028	Intermediate Similarity	NPC4370
0.8026	Intermediate Similarity	NPC470557
0.8026	Intermediate Similarity	NPC472300
0.8	Intermediate Similarity	NPC58841
0.8	Intermediate Similarity	NPC321187
0.8	Intermediate Similarity	NPC87552
0.8	Intermediate Similarity	NPC144258
0.8	Intermediate Similarity	NPC227064
0.8	Intermediate Similarity	NPC16287
0.8	Intermediate Similarity	NPC237712
0.8	Intermediate Similarity	NPC214043
0.8	Intermediate Similarity	NPC178025
0.8	Intermediate Similarity	NPC181743
0.8	Intermediate Similarity	NPC85774
0.8	Intermediate Similarity	NPC329043
0.8	Intermediate Similarity	NPC161423
0.7973	Intermediate Similarity	NPC180015
0.7973	Intermediate Similarity	NPC474488
0.7973	Intermediate Similarity	NPC56747
0.7973	Intermediate Similarity	NPC109576
0.7973	Intermediate Similarity	NPC130016
0.7971	Intermediate Similarity	NPC472306
0.7952	Intermediate Similarity	NPC262043
0.7927	Intermediate Similarity	NPC163016
0.7927	Intermediate Similarity	NPC75315
0.7927	Intermediate Similarity	NPC58063
0.7927	Intermediate Similarity	NPC476293
0.7922	Intermediate Similarity	NPC105197
0.7922	Intermediate Similarity	NPC228911
0.7922	Intermediate Similarity	NPC189485
0.791	Intermediate Similarity	NPC30215
0.7901	Intermediate Similarity	NPC469948
0.7901	Intermediate Similarity	NPC323765
0.7901	Intermediate Similarity	NPC60350
0.7901	Intermediate Similarity	NPC8571
0.7887	Intermediate Similarity	NPC168824
0.7887	Intermediate Similarity	NPC43300
0.7887	Intermediate Similarity	NPC39462
0.7887	Intermediate Similarity	NPC96812
0.7887	Intermediate Similarity	NPC189917
0.7887	Intermediate Similarity	NPC107704
0.7875	Intermediate Similarity	NPC41539
0.7867	Intermediate Similarity	NPC20025
0.7867	Intermediate Similarity	NPC159497
0.7857	Intermediate Similarity	NPC6697
0.7857	Intermediate Similarity	NPC473902
0.7848	Intermediate Similarity	NPC147066
0.7848	Intermediate Similarity	NPC475833
0.7848	Intermediate Similarity	NPC278459
0.7848	Intermediate Similarity	NPC477372
0.7838	Intermediate Similarity	NPC21944
0.7838	Intermediate Similarity	NPC304983
0.7838	Intermediate Similarity	NPC133253
0.7826	Intermediate Similarity	NPC97322
0.7826	Intermediate Similarity	NPC475795
0.7821	Intermediate Similarity	NPC476177
0.7821	Intermediate Similarity	NPC472490
0.7821	Intermediate Similarity	NPC215843
0.7821	Intermediate Similarity	NPC27817
0.7805	Intermediate Similarity	NPC195640
0.7805	Intermediate Similarity	NPC118648
0.7805	Intermediate Similarity	NPC31564
0.7805	Intermediate Similarity	NPC222613
0.7805	Intermediate Similarity	NPC145879
0.7805	Intermediate Similarity	NPC474733
0.7805	Intermediate Similarity	NPC474778
0.7805	Intermediate Similarity	NPC474732
0.7805	Intermediate Similarity	NPC327115
0.7805	Intermediate Similarity	NPC475022
0.7792	Intermediate Similarity	NPC165711
0.7778	Intermediate Similarity	NPC473246
0.7765	Intermediate Similarity	NPC218301
0.7765	Intermediate Similarity	NPC272746
0.7763	Intermediate Similarity	NPC65650
0.7763	Intermediate Similarity	NPC469803
0.7761	Intermediate Similarity	NPC267626
0.7761	Intermediate Similarity	NPC230823
0.7761	Intermediate Similarity	NPC49575
0.7761	Intermediate Similarity	NPC55004
0.775	Intermediate Similarity	NPC238991

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 NPC54123 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	1843
0.2-0.3	4548
0.3-0.4	1871
0.4-0.5	363
0.5-0.6	142
0.6-0.7	134
0.7-0.8	71
0.8-0.85	9
0.85-0.9	3
0.9-0.95	1
0.95-1	4

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9848	High Similarity	NPD4691	Approved
0.9706	High Similarity	NPD4058	Approved
0.9697	High Similarity	NPD4137	Phase 3
0.9552	High Similarity	NPD4747	Approved
0.9143	High Similarity	NPD4687	Approved
0.8971	High Similarity	NPD3621	Clinical (unspecified phase)
0.8873	High Similarity	NPD5733	Approved
0.8857	High Similarity	NPD5276	Approved
0.8333	Intermediate Similarity	NPD3527	Clinical (unspecified phase)
0.8205	Intermediate Similarity	NPD4223	Phase 3
0.8205	Intermediate Similarity	NPD4221	Approved
0.8025	Intermediate Similarity	NPD5690	Phase 2
0.8	Intermediate Similarity	NPD3133	Approved
0.8	Intermediate Similarity	NPD4197	Approved
0.8	Intermediate Similarity	NPD3666	Approved
0.8	Intermediate Similarity	NPD3665	Phase 1
0.7922	Intermediate Similarity	NPD3617	Approved
0.7901	Intermediate Similarity	NPD5329	Approved
0.7821	Intermediate Similarity	NPD4195	Approved
0.7805	Intermediate Similarity	NPD6684	Approved
0.7805	Intermediate Similarity	NPD4138	Approved
0.7805	Intermediate Similarity	NPD4693	Phase 3
0.7805	Intermediate Similarity	NPD5205	Approved
0.7805	Intermediate Similarity	NPD4690	Approved
0.7805	Intermediate Similarity	NPD4689	Approved
0.7805	Intermediate Similarity	NPD3618	Phase 1
0.7805	Intermediate Similarity	NPD4688	Approved
0.7805	Intermediate Similarity	NPD3574	Clinical (unspecified phase)
0.7805	Intermediate Similarity	NPD7334	Approved
0.7805	Intermediate Similarity	NPD7146	Approved
0.7805	Intermediate Similarity	NPD7521	Approved
0.7805	Intermediate Similarity	NPD6409	Approved
0.7805	Intermediate Similarity	NPD5330	Approved
0.7765	Intermediate Similarity	NPD6079	Approved
0.775	Intermediate Similarity	NPD3667	Approved
0.7722	Intermediate Similarity	NPD4695	Discontinued
0.7647	Intermediate Similarity	NPD287	Approved
0.7625	Intermediate Similarity	NPD8028	Phase 2
0.7619	Intermediate Similarity	NPD6903	Approved
0.7619	Intermediate Similarity	NPD6672	Approved
0.7619	Intermediate Similarity	NPD7513	Clinical (unspecified phase)
0.7619	Intermediate Similarity	NPD5737	Approved
0.7619	Intermediate Similarity	NPD5208	Approved
0.759	Intermediate Similarity	NPD4519	Discontinued
0.759	Intermediate Similarity	NPD4623	Approved
0.759	Intermediate Similarity	NPD4694	Approved
0.759	Intermediate Similarity	NPD5280	Approved
0.7561	Intermediate Similarity	NPD4786	Approved
0.7561	Intermediate Similarity	NPD3668	Phase 3
0.7529	Intermediate Similarity	NPD6904	Approved
0.7529	Intermediate Similarity	NPD5328	Approved
0.7529	Intermediate Similarity	NPD4753	Phase 2
0.7529	Intermediate Similarity	NPD6673	Approved
0.7529	Intermediate Similarity	NPD6080	Approved
0.75	Intermediate Similarity	NPD3573	Approved
0.75	Intermediate Similarity	NPD5210	Approved
0.75	Intermediate Similarity	NPD4629	Approved
0.7442	Intermediate Similarity	NPD5207	Approved
0.7416	Intermediate Similarity	NPD5222	Approved
0.7416	Intermediate Similarity	NPD5221	Approved
0.7416	Intermediate Similarity	NPD5220	Clinical (unspecified phase)
0.7381	Intermediate Similarity	NPD5279	Phase 3
0.7381	Intermediate Similarity	NPD6098	Approved
0.7356	Intermediate Similarity	NPD5281	Approved
0.7356	Intermediate Similarity	NPD5694	Approved
0.7356	Intermediate Similarity	NPD5284	Approved
0.7356	Intermediate Similarity	NPD5693	Phase 1
0.7333	Intermediate Similarity	NPD5173	Approved
0.7273	Intermediate Similarity	NPD4202	Approved
0.7241	Intermediate Similarity	NPD5692	Phase 3
0.7191	Intermediate Similarity	NPD6001	Approved
0.7174	Intermediate Similarity	NPD4696	Approved
0.7174	Intermediate Similarity	NPD5286	Approved
0.7174	Intermediate Similarity	NPD5285	Approved
0.7159	Intermediate Similarity	NPD6050	Approved
0.7111	Intermediate Similarity	NPD6356	Clinical (unspecified phase)
0.7097	Intermediate Similarity	NPD5223	Approved
0.7045	Intermediate Similarity	NPD4096	Approved
0.7033	Intermediate Similarity	NPD4697	Phase 3
0.7024	Intermediate Similarity	NPD4788	Approved
0.7021	Intermediate Similarity	NPD5091	Approved
0.7021	Intermediate Similarity	NPD4633	Approved
0.7021	Intermediate Similarity	NPD5224	Approved
0.7021	Intermediate Similarity	NPD5226	Approved
0.7021	Intermediate Similarity	NPD5211	Phase 2
0.7021	Intermediate Similarity	NPD5225	Approved
0.7011	Intermediate Similarity	NPD4518	Approved
0.6988	Remote Similarity	NPD4692	Approved
0.6988	Remote Similarity	NPD4139	Approved
0.6957	Remote Similarity	NPD4755	Approved
0.6957	Remote Similarity	NPD6083	Phase 2
0.6957	Remote Similarity	NPD6084	Phase 2
0.6947	Remote Similarity	NPD5174	Approved
0.6947	Remote Similarity	NPD5175	Approved
0.6923	Remote Similarity	NPD5695	Phase 3
0.6905	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6889	Remote Similarity	NPD6399	Phase 3
0.6889	Remote Similarity	NPD5133	Approved
0.6882	Remote Similarity	NPD5696	Approved
0.6875	Remote Similarity	NPD5141	Approved
0.6809	Remote Similarity	NPD4700	Approved
0.6778	Remote Similarity	NPD7515	Phase 2
0.6774	Remote Similarity	NPD3495	Discontinued
0.675	Remote Similarity	NPD4784	Approved
0.675	Remote Similarity	NPD4785	Approved
0.6742	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6739	Remote Similarity	NPD5654	Approved
0.6735	Remote Similarity	NPD6614	Approved
0.6735	Remote Similarity	NPD5697	Approved
0.6709	Remote Similarity	NPD4243	Approved
0.6667	Remote Similarity	NPD1694	Approved
0.6667	Remote Similarity	NPD6011	Approved
0.6667	Remote Similarity	NPD6899	Approved
0.6667	Remote Similarity	NPD5168	Approved
0.6667	Remote Similarity	NPD6881	Approved
0.6667	Remote Similarity	NPD4730	Approved
0.6667	Remote Similarity	NPD4729	Approved
0.663	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.663	Remote Similarity	NPD7748	Approved
0.663	Remote Similarity	NPD7900	Approved
0.66	Remote Similarity	NPD6012	Approved
0.66	Remote Similarity	NPD6013	Approved
0.66	Remote Similarity	NPD6014	Approved
0.6598	Remote Similarity	NPD4754	Approved
0.6598	Remote Similarity	NPD6052	Approved
0.6596	Remote Similarity	NPD5959	Approved
0.6585	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6535	Remote Similarity	NPD7102	Approved
0.6535	Remote Similarity	NPD6883	Approved
0.6535	Remote Similarity	NPD5135	Approved
0.6535	Remote Similarity	NPD5249	Phase 3
0.6535	Remote Similarity	NPD5250	Approved
0.6535	Remote Similarity	NPD5251	Approved
0.6535	Remote Similarity	NPD5169	Approved
0.6535	Remote Similarity	NPD5247	Approved
0.6535	Remote Similarity	NPD5248	Approved
0.6535	Remote Similarity	NPD5134	Clinical (unspecified phase)
0.6535	Remote Similarity	NPD4634	Approved
0.6535	Remote Similarity	NPD7290	Approved
0.65	Remote Similarity	NPD5128	Approved
0.6494	Remote Similarity	NPD7331	Phase 2
0.6489	Remote Similarity	NPD7614	Phase 1
0.6489	Remote Similarity	NPD7732	Phase 3
0.6471	Remote Similarity	NPD6847	Approved
0.6471	Remote Similarity	NPD6649	Approved
0.6471	Remote Similarity	NPD6869	Approved
0.6471	Remote Similarity	NPD5127	Approved
0.6471	Remote Similarity	NPD5217	Approved
0.6471	Remote Similarity	NPD5215	Approved
0.6471	Remote Similarity	NPD6617	Approved
0.6471	Remote Similarity	NPD5216	Approved
0.6471	Remote Similarity	NPD8130	Phase 1
0.6471	Remote Similarity	NPD6650	Approved
0.6465	Remote Similarity	NPD6008	Approved
0.6465	Remote Similarity	NPD5739	Approved
0.6465	Remote Similarity	NPD7128	Approved
0.6465	Remote Similarity	NPD6675	Approved
0.6465	Remote Similarity	NPD6402	Approved
0.6465	Remote Similarity	NPD4768	Approved
0.6465	Remote Similarity	NPD4767	Approved
0.6463	Remote Similarity	NPD4190	Phase 3
0.6463	Remote Similarity	NPD6942	Approved
0.6463	Remote Similarity	NPD7339	Approved
0.6463	Remote Similarity	NPD5275	Approved
0.6458	Remote Similarity	NPD6404	Discontinued
0.6452	Remote Similarity	NPD5769	Clinical (unspecified phase)
0.6421	Remote Similarity	NPD7902	Approved
0.6408	Remote Similarity	NPD8297	Approved
0.6408	Remote Similarity	NPD6882	Approved
0.64	Remote Similarity	NPD5701	Approved
0.64	Remote Similarity	NPD6412	Phase 2
0.6354	Remote Similarity	NPD5290	Discontinued
0.6346	Remote Similarity	NPD4632	Approved
0.6344	Remote Similarity	NPD7631	Approved
0.6337	Remote Similarity	NPD7320	Approved
0.6292	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6286	Remote Similarity	NPD5167	Approved
0.6279	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.6275	Remote Similarity	NPD6373	Approved
0.6275	Remote Similarity	NPD6372	Approved
0.6237	Remote Similarity	NPD7609	Phase 3
0.6235	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6226	Remote Similarity	NPD6868	Approved
0.619	Remote Similarity	NPD7094	Approved
0.619	Remote Similarity	NPD6858	Approved
0.6186	Remote Similarity	NPD7638	Approved
0.6184	Remote Similarity	NPD4192	Approved
0.6184	Remote Similarity	NPD4194	Approved
0.6184	Remote Similarity	NPD4191	Approved
0.6184	Remote Similarity	NPD4193	Approved
0.6173	Remote Similarity	NPD7143	Approved
0.6173	Remote Similarity	NPD7144	Approved
0.6173	Remote Similarity	NPD6938	Clinical (unspecified phase)
0.6173	Remote Similarity	NPD6939	Phase 2
0.6168	Remote Similarity	NPD6317	Approved
0.6168	Remote Similarity	NPD7115	Discovery
0.6168	Remote Similarity	NPD6009	Approved
0.6154	Remote Similarity	NPD7341	Phase 2
0.6154	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD6401	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