NPASS Compound

Structure

NPC476169 OpenBabel07101719242D 28 31 0 0 1 0 0 0 0 0999 V2000 -0.2588 -1.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7934 -0.3912 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 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8102 2.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3619 1.2235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7229 1.0341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0690 1.9306 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8442 3.1554 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 5.3960 1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1371 2.4483 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 4.1712 2.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 8.0349 1.6718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5854 4.1213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9124 3.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3336 2.9914 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6888 0.7753 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 20 1 0 0 0 0 2 20 1 0 0 0 0 3 26 1 0 0 0 0 4 5 2 0 0 0 0 4 13 1 0 0 0 0 5 15 1 0 0 0 0 6 7 2 0 0 0 0 6 12 1 0 0 0 0 7 20 1 0 0 0 0 8 11 2 0 0 0 0 8 14 1 0 0 0 0 9 11 1 0 0 0 0 9 16 2 0 0 0 0 10 21 1 0 0 0 0 10 27 1 0 0 0 0 11 22 1 0 0 0 0 12 15 2 0 0 0 0 12 18 1 0 0 0 0 13 18 2 0 0 0 0 13 21 1 0 0 0 0 14 17 2 0 0 0 0 14 23 1 0 0 0 0 15 28 1 0 0 0 0 16 17 1 0 0 0 0 16 27 1 0 0 0 0 17 19 1 0 0 0 0 18 26 1 0 0 0 0 19 21 1 0 0 0 0 19 24 2 0 0 0 0 20 28 1 0 0 0 0 21 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	384.12
Volume:	377.986
LogP:	3.534
LogD:	3.44
LogS:	-3.652
# Rotatable Bonds:	2
TPSA:	105.45
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.731
Synthetic Accessibility Score:	3.729
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.794
MDCK Permeability:	1.688821976131294e-05
Pgp-inhibitor:	0.011
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.05
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	98.30818939208984%
Volume Distribution (VD):	0.602
Pgp-substrate:	1.693629503250122%

ADMET: Metabolism

CYP1A2-inhibitor:	0.825
CYP1A2-substrate:	0.627
CYP2C19-inhibitor:	0.503
CYP2C19-substrate:	0.47
CYP2C9-inhibitor:	0.618
CYP2C9-substrate:	0.887
CYP2D6-inhibitor:	0.791
CYP2D6-substrate:	0.258
CYP3A4-inhibitor:	0.805
CYP3A4-substrate:	0.642

ADMET: Excretion

Clearance (CL):	4.665
Half-life (T1/2):	0.314

ADMET: Toxicity

hERG Blockers:	0.089
Human Hepatotoxicity (H-HT):	0.296
Drug-inuced Liver Injury (DILI):	0.387
AMES Toxicity:	0.359
Rat Oral Acute Toxicity:	0.29
Maximum Recommended Daily Dose:	0.845
Skin Sensitization:	0.406
Carcinogencity:	0.763
Eye Corrosion:	0.003
Eye Irritation:	0.027
Respiratory Toxicity:	0.482

Download Data

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

Natural Product: NPC476169

Natural Product ID:	NPC476169
*Common Name:**	Sophoronol
IUPAC Name:	3,5,7-trihydroxy-3-(5-methoxy-2,2-dimethylchromen-6-yl)-2H-chromen-4-one
Synonyms:	Sophoronol
Standard InCHIKey:	SYJLLCMGTNPNAB-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H20O7/c1-20(2)7-6-12-15(28-20)5-4-13(18(12)26-3)21(25)10-27-16-9-11(22)8-14(23)17(16)19(21)24/h4-9,22-23,25H,10H2,1-3H3
SMILES:	CC1(C=CC2=C(O1)C=CC(=C2OC)C3(COC4=CC(=CC(=C4C3=O)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL550446
PubChem CID:	15138471
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001827] Isoflavanones [CHEMONTID:0003525] 3'-prenylated isoflavanones

*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
NPO3544	Sophora mollis	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[19572738]
NPO3544	Sophora mollis	Species	Fabaceae	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
Others	1

Activity Type	# Activity
Cell Line	1
Organism	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1161	Cell Line	CHO	Cricetulus griseus	IC50	=	222700.0	nM	PMID[573222]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	114500.0	nM	PMID[573222]
NPT2	Others	Unspecified		Ratio IC50	=	2.0	n.a.	PMID[573222]

☑ 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 NPC476169 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	393
0.1-0.2	1536
0.2-0.3	3715
0.3-0.4	9349
0.4-0.5	9024
0.5-0.6	3683
0.6-0.7	5316
0.7-0.8	5204
0.8-0.85	2683
0.85-0.9	1453
0.9-0.95	305
0.95-1	36

Similarity Score	Similarity Level	Natural Product ID
0.9864	High Similarity	NPC210597
0.9797	High Similarity	NPC209760
0.9797	High Similarity	NPC100134
0.9732	High Similarity	NPC304207
0.9732	High Similarity	NPC48579
0.9732	High Similarity	NPC471116
0.9732	High Similarity	NPC207809
0.9732	High Similarity	NPC217706
0.9732	High Similarity	NPC259710
0.9667	High Similarity	NPC146636
0.9664	High Similarity	NPC236756
0.9664	High Similarity	NPC311579
0.9664	High Similarity	NPC248793
0.9664	High Similarity	NPC180301
0.9662	High Similarity	NPC471229
0.966	High Similarity	NPC277032
0.96	High Similarity	NPC111341
0.96	High Similarity	NPC304745
0.9595	High Similarity	NPC471115
0.9595	High Similarity	NPC29777
0.9595	High Similarity	NPC267117
0.9592	High Similarity	NPC296869
0.9533	High Similarity	NPC472583
0.9533	High Similarity	NPC7989
0.9533	High Similarity	NPC469405
0.9533	High Similarity	NPC268193
0.9533	High Similarity	NPC203080
0.9533	High Similarity	NPC223701
0.953	High Similarity	NPC262039
0.953	High Similarity	NPC278476
0.953	High Similarity	NPC254412
0.953	High Similarity	NPC319910
0.953	High Similarity	NPC262038
0.9524	High Similarity	NPC472918
0.9467	High Similarity	NPC475790
0.9467	High Similarity	NPC217149
0.9467	High Similarity	NPC150123
0.9467	High Similarity	NPC10807
0.9467	High Similarity	NPC161881
0.9467	High Similarity	NPC35567
0.9467	High Similarity	NPC243171
0.9467	High Similarity	NPC244583
0.9467	High Similarity	NPC216035
0.9467	High Similarity	NPC138288
0.9467	High Similarity	NPC56232
0.9467	High Similarity	NPC171651
0.9463	High Similarity	NPC105136
0.9459	High Similarity	NPC244407
0.9456	High Similarity	NPC124729
0.9412	High Similarity	NPC311574
0.9412	High Similarity	NPC264932
0.9408	High Similarity	NPC20530
0.9408	High Similarity	NPC10754
0.9408	High Similarity	NPC215917
0.9404	High Similarity	NPC20907
0.9404	High Similarity	NPC88983
0.9404	High Similarity	NPC293286
0.9404	High Similarity	NPC244250
0.94	High Similarity	NPC477897
0.94	High Similarity	NPC244577
0.94	High Similarity	NPC328740
0.94	High Similarity	NPC263384
0.94	High Similarity	NPC472422
0.94	High Similarity	NPC472636
0.94	High Similarity	NPC472420
0.94	High Similarity	NPC474021
0.94	High Similarity	NPC289774
0.94	High Similarity	NPC209846
0.94	High Similarity	NPC471677
0.94	High Similarity	NPC471675
0.94	High Similarity	NPC474023
0.94	High Similarity	NPC471676
0.9392	High Similarity	NPC166757
0.9392	High Similarity	NPC308200
0.9392	High Similarity	NPC473077
0.9392	High Similarity	NPC14001
0.9392	High Similarity	NPC296998
0.9388	High Similarity	NPC216538
0.9388	High Similarity	NPC273538
0.9359	High Similarity	NPC62261
0.9355	High Similarity	NPC474162
0.9355	High Similarity	NPC474150
0.9351	High Similarity	NPC172687
0.9346	High Similarity	NPC210048
0.9342	High Similarity	NPC477958
0.9342	High Similarity	NPC470681
0.9342	High Similarity	NPC477530
0.9338	High Similarity	NPC476238
0.9338	High Similarity	NPC31627
0.9338	High Similarity	NPC473996
0.9338	High Similarity	NPC327269
0.9333	High Similarity	NPC472633
0.9333	High Similarity	NPC61258
0.9329	High Similarity	NPC145467
0.9329	High Similarity	NPC39195
0.9329	High Similarity	NPC266572
0.9324	High Similarity	NPC111786
0.9324	High Similarity	NPC20488
0.9324	High Similarity	NPC5820
0.9324	High Similarity	NPC176229
0.9324	High Similarity	NPC229190
0.9324	High Similarity	NPC267375
0.9324	High Similarity	NPC214774
0.9324	High Similarity	NPC88964
0.9324	High Similarity	NPC470647
0.9324	High Similarity	NPC142405
0.9324	High Similarity	NPC312973
0.9324	High Similarity	NPC475052
0.9324	High Similarity	NPC54577
0.9324	High Similarity	NPC195621
0.9324	High Similarity	NPC178343
0.9324	High Similarity	NPC220418
0.9324	High Similarity	NPC83357
0.9324	High Similarity	NPC246948
0.9324	High Similarity	NPC67805
0.9324	High Similarity	NPC306488
0.9324	High Similarity	NPC301276
0.932	High Similarity	NPC190637
0.932	High Similarity	NPC212932
0.932	High Similarity	NPC293053
0.932	High Similarity	NPC9117
0.932	High Similarity	NPC219915
0.932	High Similarity	NPC24821
0.9295	High Similarity	NPC472625
0.9295	High Similarity	NPC183672
0.9276	High Similarity	NPC109594
0.9276	High Similarity	NPC326592
0.9276	High Similarity	NPC112701
0.9272	High Similarity	NPC472580
0.9267	High Similarity	NPC470461
0.9267	High Similarity	NPC5173
0.9267	High Similarity	NPC471114
0.9267	High Similarity	NPC473016
0.9267	High Similarity	NPC472628
0.9262	High Similarity	NPC201731
0.9262	High Similarity	NPC472627
0.9262	High Similarity	NPC44721
0.9262	High Similarity	NPC23728
0.9262	High Similarity	NPC104406
0.9262	High Similarity	NPC176869
0.9262	High Similarity	NPC237635
0.9262	High Similarity	NPC40086
0.9262	High Similarity	NPC79469
0.9262	High Similarity	NPC3779
0.9262	High Similarity	NPC24673
0.9262	High Similarity	NPC476182
0.9262	High Similarity	NPC110303
0.9262	High Similarity	NPC283234
0.9262	High Similarity	NPC211466
0.9262	High Similarity	NPC97716
0.9262	High Similarity	NPC122828
0.9262	High Similarity	NPC85773
0.9257	High Similarity	NPC326500
0.9257	High Similarity	NPC234629
0.9257	High Similarity	NPC271288
0.9257	High Similarity	NPC311144
0.9257	High Similarity	NPC311741
0.9252	High Similarity	NPC200694
0.9252	High Similarity	NPC473042
0.9231	High Similarity	NPC472402
0.9231	High Similarity	NPC131745
0.9231	High Similarity	NPC219861
0.9226	High Similarity	NPC475784
0.9226	High Similarity	NPC471976
0.9226	High Similarity	NPC118256
0.9226	High Similarity	NPC119209
0.9226	High Similarity	NPC192686
0.9221	High Similarity	NPC473272
0.9221	High Similarity	NPC282390
0.9221	High Similarity	NPC284820
0.9221	High Similarity	NPC161650
0.9221	High Similarity	NPC65504
0.9221	High Similarity	NPC281137
0.9211	High Similarity	NPC142527
0.9211	High Similarity	NPC477957
0.9211	High Similarity	NPC285623
0.9205	High Similarity	NPC124478
0.9205	High Similarity	NPC177308
0.9205	High Similarity	NPC472421
0.92	High Similarity	NPC160821
0.92	High Similarity	NPC10097
0.92	High Similarity	NPC132592
0.92	High Similarity	NPC470460
0.92	High Similarity	NPC6511
0.92	High Similarity	NPC161191
0.9195	High Similarity	NPC472629
0.9195	High Similarity	NPC299011
0.9195	High Similarity	NPC477955
0.9195	High Similarity	NPC470458
0.9195	High Similarity	NPC474302
0.9189	High Similarity	NPC18585
0.9189	High Similarity	NPC113770
0.9189	High Similarity	NPC166138
0.9189	High Similarity	NPC38219
0.9189	High Similarity	NPC478086
0.9189	High Similarity	NPC316816
0.9189	High Similarity	NPC214166
0.9189	High Similarity	NPC158874
0.9189	High Similarity	NPC106985
0.9182	High Similarity	NPC177480

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 NPC476169 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	345
0.1-0.2	914
0.2-0.3	1611
0.3-0.4	2647
0.4-0.5	1867
0.5-0.6	1112
0.6-0.7	445
0.7-0.8	156
0.8-0.85	32
0.85-0.9	20
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9388	High Similarity	NPD4378	Clinical (unspecified phase)
0.9205	High Similarity	NPD4380	Phase 2
0.9097	High Similarity	NPD7075	Discontinued
0.9026	High Similarity	NPD7096	Clinical (unspecified phase)
0.9026	High Similarity	NPD2393	Clinical (unspecified phase)
0.8944	High Similarity	NPD7804	Clinical (unspecified phase)
0.8874	High Similarity	NPD7410	Clinical (unspecified phase)
0.8854	High Similarity	NPD4381	Clinical (unspecified phase)
0.8846	High Similarity	NPD8443	Clinical (unspecified phase)
0.8839	High Similarity	NPD6801	Discontinued
0.8839	High Similarity	NPD1934	Approved
0.8784	High Similarity	NPD1550	Clinical (unspecified phase)
0.8784	High Similarity	NPD1552	Clinical (unspecified phase)
0.8782	High Similarity	NPD2801	Approved
0.8758	High Similarity	NPD6166	Phase 2
0.8758	High Similarity	NPD6167	Clinical (unspecified phase)
0.8758	High Similarity	NPD6168	Clinical (unspecified phase)
0.8725	High Similarity	NPD1549	Phase 2
0.8693	High Similarity	NPD1512	Approved
0.8684	High Similarity	NPD6799	Approved
0.8671	High Similarity	NPD3882	Suspended
0.8654	High Similarity	NPD7411	Suspended
0.8649	High Similarity	NPD1510	Phase 2
0.8608	High Similarity	NPD3817	Phase 2
0.8591	High Similarity	NPD2796	Approved
0.859	High Similarity	NPD6599	Discontinued
0.8562	High Similarity	NPD1511	Approved
0.8544	High Similarity	NPD7819	Suspended
0.8509	High Similarity	NPD5494	Approved
0.8494	Intermediate Similarity	NPD6797	Phase 2
0.8457	Intermediate Similarity	NPD6959	Discontinued
0.8443	Intermediate Similarity	NPD7251	Discontinued
0.8415	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.8397	Intermediate Similarity	NPD5403	Approved
0.8393	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.8393	Intermediate Similarity	NPD7808	Phase 3
0.8378	Intermediate Similarity	NPD1240	Approved
0.8375	Intermediate Similarity	NPD5402	Approved
0.8373	Intermediate Similarity	NPD7054	Approved
0.8323	Intermediate Similarity	NPD7768	Phase 2
0.8323	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8323	Intermediate Similarity	NPD7074	Phase 3
0.8323	Intermediate Similarity	NPD7472	Approved
0.8313	Intermediate Similarity	NPD3818	Discontinued
0.8301	Intermediate Similarity	NPD2800	Approved
0.8272	Intermediate Similarity	NPD3749	Approved
0.8269	Intermediate Similarity	NPD5401	Approved
0.8267	Intermediate Similarity	NPD1607	Approved
0.8247	Intermediate Similarity	NPD3750	Approved
0.8182	Intermediate Similarity	NPD6232	Discontinued
0.8144	Intermediate Similarity	NPD7473	Discontinued
0.8118	Intermediate Similarity	NPD6559	Discontinued
0.8065	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.8059	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.805	Intermediate Similarity	NPD920	Approved
0.8047	Intermediate Similarity	NPD5844	Phase 1
0.8038	Intermediate Similarity	NPD2533	Approved
0.8038	Intermediate Similarity	NPD2534	Approved
0.8038	Intermediate Similarity	NPD2532	Approved
0.8012	Intermediate Similarity	NPD1247	Approved
0.8011	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7965	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7925	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7922	Intermediate Similarity	NPD3748	Approved
0.7922	Intermediate Similarity	NPD2799	Discontinued
0.7898	Intermediate Similarity	NPD4628	Phase 3
0.7892	Intermediate Similarity	NPD919	Approved
0.7882	Intermediate Similarity	NPD3751	Discontinued
0.7881	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7881	Intermediate Similarity	NPD2313	Discontinued
0.7871	Intermediate Similarity	NPD2935	Discontinued
0.7871	Intermediate Similarity	NPD1551	Phase 2
0.7867	Intermediate Similarity	NPD4908	Phase 1
0.7866	Intermediate Similarity	NPD1465	Phase 2
0.7857	Intermediate Similarity	NPD3787	Discontinued
0.7849	Intermediate Similarity	NPD5953	Discontinued
0.7836	Intermediate Similarity	NPD7286	Phase 2
0.7834	Intermediate Similarity	NPD1243	Approved
0.7833	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7821	Intermediate Similarity	NPD2344	Approved
0.7821	Intermediate Similarity	NPD4360	Phase 2
0.7821	Intermediate Similarity	NPD4363	Phase 3
0.7811	Intermediate Similarity	NPD3926	Phase 2
0.7799	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7792	Intermediate Similarity	NPD6651	Approved
0.7785	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7756	Intermediate Similarity	NPD6100	Approved
0.7756	Intermediate Similarity	NPD6099	Approved
0.773	Intermediate Similarity	NPD3226	Approved
0.7707	Intermediate Similarity	NPD2346	Discontinued
0.7705	Intermediate Similarity	NPD6782	Approved
0.7705	Intermediate Similarity	NPD6778	Approved
0.7705	Intermediate Similarity	NPD6777	Approved
0.7705	Intermediate Similarity	NPD6776	Approved
0.7705	Intermediate Similarity	NPD6781	Approved
0.7705	Intermediate Similarity	NPD6779	Approved
0.7705	Intermediate Similarity	NPD6780	Approved
0.7692	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7662	Intermediate Similarity	NPD943	Approved
0.7647	Intermediate Similarity	NPD7584	Approved
0.764	Intermediate Similarity	NPD7390	Discontinued
0.7635	Intermediate Similarity	NPD1610	Phase 2
0.7625	Intermediate Similarity	NPD2309	Approved
0.7614	Intermediate Similarity	NPD8312	Approved
0.7614	Intermediate Similarity	NPD8313	Approved
0.7613	Intermediate Similarity	NPD5124	Phase 1
0.7613	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.7584	Intermediate Similarity	NPD8150	Discontinued
0.7584	Intermediate Similarity	NPD8434	Phase 2
0.7581	Intermediate Similarity	NPD7435	Discontinued
0.758	Intermediate Similarity	NPD7033	Discontinued
0.7562	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7558	Intermediate Similarity	NPD2403	Approved
0.7548	Intermediate Similarity	NPD1613	Approved
0.7548	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7547	Intermediate Similarity	NPD2424	Discontinued
0.7544	Intermediate Similarity	NPD5710	Approved
0.7544	Intermediate Similarity	NPD5711	Approved
0.7532	Intermediate Similarity	NPD6798	Discontinued
0.7532	Intermediate Similarity	NPD3268	Approved
0.753	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7528	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7517	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7516	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7515	Intermediate Similarity	NPD7458	Discontinued
0.7514	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD2798	Approved
0.75	Intermediate Similarity	NPD6355	Discontinued
0.7487	Intermediate Similarity	NPD7697	Approved
0.7487	Intermediate Similarity	NPD7698	Approved
0.7487	Intermediate Similarity	NPD7696	Phase 3
0.7486	Intermediate Similarity	NPD4362	Clinical (unspecified phase)
0.7486	Intermediate Similarity	NPD4361	Phase 2
0.7483	Intermediate Similarity	NPD1548	Phase 1
0.7468	Intermediate Similarity	NPD4625	Phase 3
0.7468	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7451	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7447	Intermediate Similarity	NPD7870	Phase 2
0.7447	Intermediate Similarity	NPD7871	Phase 2
0.744	Intermediate Similarity	NPD8455	Phase 2
0.7436	Intermediate Similarity	NPD4060	Phase 1
0.7434	Intermediate Similarity	NPD1203	Approved
0.7434	Intermediate Similarity	NPD2797	Approved
0.7432	Intermediate Similarity	NPD6534	Approved
0.7432	Intermediate Similarity	NPD6535	Approved
0.7421	Intermediate Similarity	NPD7701	Phase 2
0.7403	Intermediate Similarity	NPD6832	Phase 2
0.7403	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7399	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7389	Intermediate Similarity	NPD230	Phase 1
0.7378	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7372	Intermediate Similarity	NPD6233	Phase 2
0.7358	Intermediate Similarity	NPD4308	Phase 3
0.7356	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7344	Intermediate Similarity	NPD7874	Approved
0.7344	Intermediate Similarity	NPD7875	Clinical (unspecified phase)
0.7341	Intermediate Similarity	NPD7229	Phase 3
0.7333	Intermediate Similarity	NPD5049	Phase 3
0.7312	Intermediate Similarity	NPD7699	Phase 2
0.7312	Intermediate Similarity	NPD7700	Phase 2
0.7308	Intermediate Similarity	NPD4287	Approved
0.7306	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7306	Intermediate Similarity	NPD7801	Approved
0.7306	Intermediate Similarity	NPD7783	Phase 2
0.7305	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7301	Intermediate Similarity	NPD2354	Approved
0.7301	Intermediate Similarity	NPD6190	Approved
0.7294	Intermediate Similarity	NPD4288	Approved
0.7292	Intermediate Similarity	NPD8151	Discontinued
0.7289	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7285	Intermediate Similarity	NPD422	Phase 1
0.7284	Intermediate Similarity	NPD1652	Phase 2
0.7283	Intermediate Similarity	NPD7199	Phase 2
0.7278	Intermediate Similarity	NPD6844	Discontinued
0.7278	Intermediate Similarity	NPD1933	Approved
0.7278	Intermediate Similarity	NPD447	Suspended
0.7267	Intermediate Similarity	NPD6234	Discontinued
0.7267	Intermediate Similarity	NPD1471	Phase 3
0.7267	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7255	Intermediate Similarity	NPD3225	Approved
0.7249	Intermediate Similarity	NPD6823	Phase 2
0.7247	Intermediate Similarity	NPD3823	Discontinued
0.7244	Intermediate Similarity	NPD3027	Phase 3
0.724	Intermediate Similarity	NPD7585	Approved
0.7237	Intermediate Similarity	NPD9717	Approved
0.7219	Intermediate Similarity	NPD5889	Approved
0.7219	Intermediate Similarity	NPD5890	Approved
0.7208	Intermediate Similarity	NPD3267	Approved
0.7208	Intermediate Similarity	NPD3266	Approved
0.7207	Intermediate Similarity	NPD7685	Pre-registration
0.7197	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7197	Intermediate Similarity	NPD3764	Approved
0.7195	Intermediate Similarity	NPD3887	Approved
0.7191	Intermediate Similarity	NPD1729	Discontinued
0.719	Intermediate Similarity	NPD4749	Approved
0.7188	Intermediate Similarity	NPD7583	Approved
0.7178	Intermediate Similarity	NPD2654	Approved
0.7176	Intermediate Similarity	NPD37	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