NPASS Compound

Structure

CID129684 OpenBabel06191715482D 23 25 0 0 1 0 0 0 0 0999 V2000 -2.5981 -1.5000 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 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 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 0.0000 -2.0000 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 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 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 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 2 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 3.4641 1.0000 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 22 1 0 0 0 0 3 4 2 0 0 0 0 3 9 1 0 0 0 0 4 11 1 0 0 0 0 5 6 2 0 0 0 0 5 10 1 0 0 0 0 6 13 1 0 0 0 0 7 9 2 0 0 0 0 7 14 1 0 0 0 0 8 12 1 0 0 0 0 8 23 1 0 0 0 0 9 18 1 0 0 0 0 10 17 2 0 0 0 0 11 14 2 0 0 0 0 11 15 1 0 0 0 0 12 10 1 1 0 0 0 12 15 1 0 0 0 0 13 16 2 0 0 0 0 13 21 1 0 0 0 0 14 23 1 0 0 0 0 15 19 2 0 0 0 0 16 17 1 0 0 0 0 16 20 1 0 0 0 0 17 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	316.09
Volume:	311.205
LogP:	2.328
LogD:	2.149
LogS:	-3.976
# Rotatable Bonds:	3
TPSA:	85.22
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.905
Synthetic Accessibility Score:	2.964
Fsp3:	0.235
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.696
MDCK Permeability:	1.951502235897351e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.03
Plasma Protein Binding (PPB):	98.5728530883789%
Volume Distribution (VD):	0.449
Pgp-substrate:	3.7078921794891357%

ADMET: Metabolism

CYP1A2-inhibitor:	0.882
CYP1A2-substrate:	0.943
CYP2C19-inhibitor:	0.827
CYP2C19-substrate:	0.615
CYP2C9-inhibitor:	0.792
CYP2C9-substrate:	0.915
CYP2D6-inhibitor:	0.566
CYP2D6-substrate:	0.901
CYP3A4-inhibitor:	0.784
CYP3A4-substrate:	0.656

ADMET: Excretion

Clearance (CL):	8.352
Half-life (T1/2):	0.71

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.223
Drug-inuced Liver Injury (DILI):	0.472
AMES Toxicity:	0.182
Rat Oral Acute Toxicity:	0.436
Maximum Recommended Daily Dose:	0.191
Skin Sensitization:	0.63
Carcinogencity:	0.308
Eye Corrosion:	0.003
Eye Irritation:	0.245
Respiratory Toxicity:	0.193

Download Data

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

Natural Product: NPC129684

Natural Product ID:	NPC129684
*Common Name:**	(3S)-Violanone
IUPAC Name:	(3S)-7-hydroxy-3-(3-hydroxy-2,4-dimethoxyphenyl)-2,3-dihydrochromen-4-one
Synonyms:	(3S)-Violanone
Standard InCHIKey:	ILOKNKKFXJKHMB-GFCCVEGCSA-N
Standard InCHI:	InChI=1S/C17H16O6/c1-21-13-6-5-10(17(22-2)16(13)20)12-8-23-14-7-9(18)3-4-11(14)15(12)19/h3-7,12,18,20H,8H2,1-2H3/t12-/m1/s1
SMILES:	COc1c(ccc(c1O)OC)[C@H]1COc2c(C1=O)ccc(c2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL254526
PubChem CID:	44446884
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002586] O-methylated isoflavonoids [CHEMONTID:0002606] 4'-O-methylated isoflavonoids [CHEMONTID:0003651] 3'-hydroxy,4'-methoxyisoflavonoids

*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
NPO33288	Brazilian Red Propolis	Strain	n.a.	n.a.	n.a.	Brazilian	n.a.	PMID[17950610]
NPO33288	Brazilian Red Propolis	Strain	n.a.	n.a.	n.a.	Brazilian	n.a.	PMID[18440233]
NPO14114	Dalbergia parviflora	Species	Fabaceae	Eukaryota	heartwood	n.a.	n.a.	PMID[19928832]
NPO33288	Brazilian Red Propolis	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[26938776]
NPO33288	Brazilian Red Propolis	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[32525315]
NPO14114	Dalbergia parviflora	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	6
Others	9

Activity Type	# Activity
Cell Line	12
NON-MOLECULAR	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT461	Cell Line	PANC-1	Homo sapiens	CD100	>	100.0	uM	PMID[544721]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	100000.0	nM	PMID[544722]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	100000.0	nM	PMID[544722]
NPT453	Cell Line	HT-1080	Homo sapiens	IC50	>	100000.0	nM	PMID[544722]
NPT396	Cell Line	T47D	Homo sapiens	Activity	>	100.0	uM	PMID[544723]
NPT396	Cell Line	T47D	Homo sapiens	Activity	=	0.6	uM	PMID[544723]
NPT83	Cell Line	MCF7	Homo sapiens	Activity	>	100.0	uM	PMID[544723]
NPT396	Cell Line	T47D	Homo sapiens	Activity	=	8.9	uM	PMID[544723]
NPT396	Cell Line	T47D	Homo sapiens	Activity	=	2.1	uM	PMID[544723]
NPT83	Cell Line	MCF7	Homo sapiens	Activity	=	9.4	uM	PMID[544723]
NPT83	Cell Line	MCF7	Homo sapiens	Activity	=	2.1	uM	PMID[544723]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	100000.0	nM	PMID[544722]

☑ 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 NPC129684 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	409
0.1-0.2	1625
0.2-0.3	4057
0.3-0.4	9759
0.4-0.5	8253
0.5-0.6	3293
0.6-0.7	4644
0.7-0.8	5433
0.8-0.85	2769
0.85-0.9	1668
0.9-0.95	723
0.95-1	64

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC299520
0.9866	High Similarity	NPC31018
0.9866	High Similarity	NPC255807
0.9799	High Similarity	NPC469550
0.9735	High Similarity	NPC472910
0.9735	High Similarity	NPC222814
0.9735	High Similarity	NPC472913
0.9735	High Similarity	NPC472914
0.9735	High Similarity	NPC96167
0.9735	High Similarity	NPC472911
0.9735	High Similarity	NPC469584
0.9735	High Similarity	NPC181960
0.9735	High Similarity	NPC245758
0.9732	High Similarity	NPC472912
0.9732	High Similarity	NPC257648
0.9732	High Similarity	NPC477231
0.9732	High Similarity	NPC260979
0.9671	High Similarity	NPC55738
0.9669	High Similarity	NPC472916
0.9667	High Similarity	NPC18727
0.9664	High Similarity	NPC31363
0.961	High Similarity	NPC474162
0.961	High Similarity	NPC474150
0.9605	High Similarity	NPC210084
0.9605	High Similarity	NPC291508
0.9605	High Similarity	NPC67876
0.9605	High Similarity	NPC48208
0.9605	High Similarity	NPC474208
0.9605	High Similarity	NPC475267
0.9605	High Similarity	NPC99597
0.9605	High Similarity	NPC474836
0.9605	High Similarity	NPC162869
0.9605	High Similarity	NPC156057
0.9603	High Similarity	NPC57674
0.9603	High Similarity	NPC2928
0.9603	High Similarity	NPC230149
0.9603	High Similarity	NPC168247
0.9603	High Similarity	NPC472909
0.9603	High Similarity	NPC117992
0.9603	High Similarity	NPC152951
0.96	High Similarity	NPC219582
0.96	High Similarity	NPC302950
0.96	High Similarity	NPC60972
0.96	High Similarity	NPC236637
0.96	High Similarity	NPC39732
0.9597	High Similarity	NPC29231
0.9551	High Similarity	NPC235610
0.9545	High Similarity	NPC266314
0.9539	High Similarity	NPC291878
0.9539	High Similarity	NPC278778
0.9539	High Similarity	NPC235165
0.9539	High Similarity	NPC35038
0.9539	High Similarity	NPC195796
0.9539	High Similarity	NPC474638
0.9539	High Similarity	NPC255106
0.9536	High Similarity	NPC33051
0.9536	High Similarity	NPC472915
0.9536	High Similarity	NPC292214
0.9536	High Similarity	NPC88645
0.9536	High Similarity	NPC49402
0.9536	High Similarity	NPC273462
0.9536	High Similarity	NPC70433
0.9536	High Similarity	NPC206238
0.9536	High Similarity	NPC167091
0.9536	High Similarity	NPC227337
0.9536	High Similarity	NPC271779
0.953	High Similarity	NPC105512
0.9487	High Similarity	NPC472277
0.9484	High Similarity	NPC472964
0.9481	High Similarity	NPC36217
0.9481	High Similarity	NPC474960
0.9481	High Similarity	NPC472902
0.9477	High Similarity	NPC27337
0.9477	High Similarity	NPC78225
0.9477	High Similarity	NPC52530
0.9477	High Similarity	NPC471515
0.9477	High Similarity	NPC219867
0.9477	High Similarity	NPC241904
0.9477	High Similarity	NPC472963
0.9477	High Similarity	NPC161960
0.9477	High Similarity	NPC304008
0.9477	High Similarity	NPC262286
0.9477	High Similarity	NPC187745
0.9477	High Similarity	NPC472598
0.9477	High Similarity	NPC300727
0.9477	High Similarity	NPC471479
0.9477	High Similarity	NPC474055
0.9477	High Similarity	NPC36852
0.9477	High Similarity	NPC180011
0.9474	High Similarity	NPC256612
0.9474	High Similarity	NPC45849
0.9474	High Similarity	NPC200761
0.9474	High Similarity	NPC213622
0.9474	High Similarity	NPC37392
0.9474	High Similarity	NPC470327
0.9474	High Similarity	NPC256925
0.9474	High Similarity	NPC67396
0.9474	High Similarity	NPC20830
0.9474	High Similarity	NPC477503
0.947	High Similarity	NPC180234
0.947	High Similarity	NPC101996
0.947	High Similarity	NPC199100
0.947	High Similarity	NPC39007
0.947	High Similarity	NPC120537
0.947	High Similarity	NPC161277
0.9467	High Similarity	NPC338131
0.9463	High Similarity	NPC272721
0.9463	High Similarity	NPC196277
0.9463	High Similarity	NPC3036
0.9463	High Similarity	NPC43669
0.9427	High Similarity	NPC477517
0.9423	High Similarity	NPC205265
0.9423	High Similarity	NPC124038
0.9423	High Similarity	NPC472281
0.9423	High Similarity	NPC18100
0.9419	High Similarity	NPC308992
0.9419	High Similarity	NPC173137
0.9419	High Similarity	NPC134783
0.9419	High Similarity	NPC472275
0.9416	High Similarity	NPC95936
0.9416	High Similarity	NPC476242
0.9416	High Similarity	NPC250214
0.9416	High Similarity	NPC204879
0.9416	High Similarity	NPC152904
0.9412	High Similarity	NPC209614
0.9412	High Similarity	NPC471500
0.9412	High Similarity	NPC326037
0.9412	High Similarity	NPC470328
0.9412	High Similarity	NPC274730
0.9412	High Similarity	NPC265511
0.9412	High Similarity	NPC191146
0.9412	High Similarity	NPC472626
0.9412	High Similarity	NPC13858
0.9412	High Similarity	NPC320825
0.9412	High Similarity	NPC68093
0.9412	High Similarity	NPC24640
0.9412	High Similarity	NPC115853
0.9412	High Similarity	NPC472455
0.9412	High Similarity	NPC472907
0.9412	High Similarity	NPC138243
0.9408	High Similarity	NPC280937
0.9408	High Similarity	NPC231018
0.9408	High Similarity	NPC47781
0.9408	High Similarity	NPC22519
0.9408	High Similarity	NPC176775
0.9408	High Similarity	NPC255350
0.9408	High Similarity	NPC160951
0.9408	High Similarity	NPC274327
0.9408	High Similarity	NPC141212
0.9408	High Similarity	NPC472905
0.9408	High Similarity	NPC192083
0.9408	High Similarity	NPC69394
0.9408	High Similarity	NPC213896
0.9408	High Similarity	NPC183878
0.9408	High Similarity	NPC145379
0.9408	High Similarity	NPC124714
0.9404	High Similarity	NPC171010
0.9404	High Similarity	NPC117579
0.9404	High Similarity	NPC251110
0.9404	High Similarity	NPC149614
0.94	High Similarity	NPC40290
0.94	High Similarity	NPC200060
0.94	High Similarity	NPC137062
0.94	High Similarity	NPC183950
0.94	High Similarity	NPC183959
0.94	High Similarity	NPC69430
0.94	High Similarity	NPC264289
0.94	High Similarity	NPC48479
0.94	High Similarity	NPC52005
0.94	High Similarity	NPC287101
0.94	High Similarity	NPC333691
0.94	High Similarity	NPC195763
0.94	High Similarity	NPC1612
0.94	High Similarity	NPC264550
0.94	High Similarity	NPC142876
0.94	High Similarity	NPC177298
0.94	High Similarity	NPC223579
0.94	High Similarity	NPC139293
0.9396	High Similarity	NPC77378
0.9396	High Similarity	NPC470511
0.9396	High Similarity	NPC95864
0.9371	High Similarity	NPC131866
0.9363	High Similarity	NPC108433
0.9363	High Similarity	NPC234052
0.9363	High Similarity	NPC300053
0.9363	High Similarity	NPC224280
0.9363	High Similarity	NPC62261
0.9359	High Similarity	NPC472448
0.9359	High Similarity	NPC474034
0.9359	High Similarity	NPC476247
0.9359	High Similarity	NPC474033
0.9359	High Similarity	NPC201800
0.9359	High Similarity	NPC83922
0.9355	High Similarity	NPC228785
0.9355	High Similarity	NPC476980
0.9355	High Similarity	NPC119209
0.9355	High Similarity	NPC192686
0.9355	High Similarity	NPC287328
0.9355	High Similarity	NPC118256
0.9355	High Similarity	NPC470183

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 NPC129684 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	368
0.1-0.2	938
0.2-0.3	1713
0.3-0.4	2617
0.4-0.5	1763
0.5-0.6	1032
0.6-0.7	515
0.7-0.8	141
0.8-0.85	41
0.85-0.9	10
0.9-0.95	11
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.96	High Similarity	NPD1934	Approved
0.9408	High Similarity	NPD2393	Clinical (unspecified phase)
0.9408	High Similarity	NPD2801	Approved
0.9286	High Similarity	NPD3882	Suspended
0.9119	High Similarity	NPD6167	Clinical (unspecified phase)
0.9119	High Similarity	NPD6168	Clinical (unspecified phase)
0.9119	High Similarity	NPD6166	Phase 2
0.9067	High Similarity	NPD1511	Approved
0.9006	High Similarity	NPD3818	Discontinued
0.8987	High Similarity	NPD5494	Approved
0.8947	High Similarity	NPD1512	Approved
0.8917	High Similarity	NPD4868	Clinical (unspecified phase)
0.8896	High Similarity	NPD7074	Phase 3
0.8854	High Similarity	NPD3817	Phase 2
0.8834	High Similarity	NPD7054	Approved
0.878	High Similarity	NPD7472	Approved
0.8733	High Similarity	NPD1549	Phase 2
0.8718	High Similarity	NPD4380	Phase 2
0.8667	High Similarity	NPD1550	Clinical (unspecified phase)
0.8667	High Similarity	NPD1552	Clinical (unspecified phase)
0.8636	High Similarity	NPD4378	Clinical (unspecified phase)
0.8625	High Similarity	NPD7075	Discontinued
0.8625	High Similarity	NPD4381	Clinical (unspecified phase)
0.8623	High Similarity	NPD4338	Clinical (unspecified phase)
0.8614	High Similarity	NPD6797	Phase 2
0.8598	High Similarity	NPD7473	Discontinued
0.8563	High Similarity	NPD7251	Discontinued
0.8553	High Similarity	NPD7819	Suspended
0.8553	High Similarity	NPD7096	Clinical (unspecified phase)
0.8553	High Similarity	NPD1465	Phase 2
0.8533	High Similarity	NPD1510	Phase 2
0.8528	High Similarity	NPD6232	Discontinued
0.8512	High Similarity	NPD7808	Phase 3
0.85	High Similarity	NPD8443	Clinical (unspecified phase)
0.8477	Intermediate Similarity	NPD2796	Approved
0.8452	Intermediate Similarity	NPD6799	Approved
0.8393	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.8389	Intermediate Similarity	NPD1240	Approved
0.8389	Intermediate Similarity	NPD943	Approved
0.8383	Intermediate Similarity	NPD5844	Phase 1
0.8365	Intermediate Similarity	NPD6599	Discontinued
0.8313	Intermediate Similarity	NPD7411	Suspended
0.828	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.8278	Intermediate Similarity	NPD1607	Approved
0.8261	Intermediate Similarity	NPD6801	Discontinued
0.8253	Intermediate Similarity	NPD3926	Phase 2
0.8242	Intermediate Similarity	NPD6959	Discontinued
0.8166	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.816	Intermediate Similarity	NPD5402	Approved
0.8146	Intermediate Similarity	NPD1613	Approved
0.8146	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.8133	Intermediate Similarity	NPD1247	Approved
0.8129	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.8129	Intermediate Similarity	NPD6559	Discontinued
0.8121	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.8095	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.8092	Intermediate Similarity	NPD230	Phase 1
0.8061	Intermediate Similarity	NPD3749	Approved
0.8054	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.8025	Intermediate Similarity	NPD3750	Approved
0.8012	Intermediate Similarity	NPD919	Approved
0.8	Intermediate Similarity	NPD7768	Phase 2
0.7974	Intermediate Similarity	NPD447	Suspended
0.7962	Intermediate Similarity	NPD2800	Approved
0.795	Intermediate Similarity	NPD5403	Approved
0.795	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7947	Intermediate Similarity	NPD3027	Phase 3
0.7937	Intermediate Similarity	NPD2532	Approved
0.7937	Intermediate Similarity	NPD2533	Approved
0.7937	Intermediate Similarity	NPD2534	Approved
0.7935	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7917	Intermediate Similarity	NPD7199	Phase 2
0.7912	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7911	Intermediate Similarity	NPD4628	Phase 3
0.7904	Intermediate Similarity	NPD6234	Discontinued
0.7885	Intermediate Similarity	NPD2935	Discontinued
0.7885	Intermediate Similarity	NPD6100	Approved
0.7885	Intermediate Similarity	NPD1551	Phase 2
0.7885	Intermediate Similarity	NPD6099	Approved
0.7848	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7841	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7834	Intermediate Similarity	NPD2344	Approved
0.7826	Intermediate Similarity	NPD5401	Approved
0.7824	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7821	Intermediate Similarity	NPD2799	Discontinued
0.7815	Intermediate Similarity	NPD9494	Approved
0.7809	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7791	Intermediate Similarity	NPD3751	Discontinued
0.7778	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7763	Intermediate Similarity	NPD4908	Phase 1
0.7744	Intermediate Similarity	NPD3226	Approved
0.7742	Intermediate Similarity	NPD1933	Approved
0.773	Intermediate Similarity	NPD920	Approved
0.7722	Intermediate Similarity	NPD2346	Discontinued
0.7714	Intermediate Similarity	NPD7685	Pre-registration
0.7711	Intermediate Similarity	NPD37	Approved
0.7707	Intermediate Similarity	NPD3748	Approved
0.7707	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7688	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7688	Intermediate Similarity	NPD7228	Approved
0.7688	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7683	Intermediate Similarity	NPD1653	Approved
0.7679	Intermediate Similarity	NPD4966	Approved
0.7679	Intermediate Similarity	NPD4967	Phase 2
0.7679	Intermediate Similarity	NPD4965	Approved
0.767	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7667	Intermediate Similarity	NPD4379	Clinical (unspecified phase)
0.7662	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7661	Intermediate Similarity	NPD3787	Discontinued
0.7657	Intermediate Similarity	NPD5953	Discontinued
0.7654	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7651	Intermediate Similarity	NPD1610	Phase 2
0.7644	Intermediate Similarity	NPD7286	Phase 2
0.764	Intermediate Similarity	NPD2309	Approved
0.764	Intermediate Similarity	NPD6190	Approved
0.7627	Intermediate Similarity	NPD8313	Approved
0.7627	Intermediate Similarity	NPD8312	Approved
0.7624	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7616	Intermediate Similarity	NPD5242	Approved
0.7607	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.758	Intermediate Similarity	NPD6651	Approved
0.7548	Intermediate Similarity	NPD2313	Discontinued
0.7533	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7516	Intermediate Similarity	NPD1243	Approved
0.7516	Intermediate Similarity	NPD2798	Approved
0.7515	Intermediate Similarity	NPD5353	Approved
0.75	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD8434	Phase 2
0.7485	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7457	Intermediate Similarity	NPD5711	Approved
0.7457	Intermediate Similarity	NPD5710	Approved
0.7451	Intermediate Similarity	NPD1203	Approved
0.7446	Intermediate Similarity	NPD4360	Phase 2
0.7446	Intermediate Similarity	NPD4363	Phase 3
0.7439	Intermediate Similarity	NPD7390	Discontinued
0.7436	Intermediate Similarity	NPD3268	Approved
0.7419	Intermediate Similarity	NPD6832	Phase 2
0.7405	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7403	Intermediate Similarity	NPD8150	Discontinued
0.7371	Intermediate Similarity	NPD2403	Approved
0.7368	Intermediate Similarity	NPD1608	Approved
0.7368	Intermediate Similarity	NPD9269	Phase 2
0.7356	Intermediate Similarity	NPD7229	Phase 3
0.7355	Intermediate Similarity	NPD2861	Phase 2
0.734	Intermediate Similarity	NPD6776	Approved
0.734	Intermediate Similarity	NPD6780	Approved
0.734	Intermediate Similarity	NPD6781	Approved
0.734	Intermediate Similarity	NPD6779	Approved
0.734	Intermediate Similarity	NPD6778	Approved
0.734	Intermediate Similarity	NPD6782	Approved
0.734	Intermediate Similarity	NPD6777	Approved
0.7338	Intermediate Similarity	NPD2797	Approved
0.7337	Intermediate Similarity	NPD6385	Approved
0.7337	Intermediate Similarity	NPD6386	Approved
0.7337	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7321	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7321	Intermediate Similarity	NPD7458	Discontinued
0.732	Intermediate Similarity	NPD4749	Approved
0.7306	Intermediate Similarity	NPD8151	Discontinued
0.7296	Intermediate Similarity	NPD6355	Discontinued
0.7294	Intermediate Similarity	NPD6844	Discontinued
0.7278	Intermediate Similarity	NPD7549	Discontinued
0.7273	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7267	Intermediate Similarity	NPD5019	Clinical (unspecified phase)
0.7267	Intermediate Similarity	NPD1548	Phase 1
0.7267	Intermediate Similarity	NPD7033	Discontinued
0.7261	Intermediate Similarity	NPD4625	Phase 3
0.7255	Intermediate Similarity	NPD9717	Approved
0.7233	Intermediate Similarity	NPD4060	Phase 1
0.7229	Intermediate Similarity	NPD4357	Discontinued
0.7226	Intermediate Similarity	NPD1470	Approved
0.7225	Intermediate Similarity	NPD7435	Discontinued
0.7222	Intermediate Similarity	NPD7240	Approved
0.7219	Intermediate Similarity	NPD4361	Phase 2
0.7219	Intermediate Similarity	NPD4362	Clinical (unspecified phase)
0.7215	Intermediate Similarity	NPD6798	Discontinued
0.7215	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7202	Intermediate Similarity	NPD7584	Approved
0.72	Intermediate Similarity	NPD8127	Discontinued
0.72	Intermediate Similarity	NPD5536	Phase 2
0.7178	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7178	Intermediate Similarity	NPD7266	Discontinued
0.7171	Intermediate Similarity	NPD17	Approved
0.716	Intermediate Similarity	NPD4308	Phase 3
0.7152	Intermediate Similarity	NPD8166	Discontinued
0.7152	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD4110	Phase 3
0.7151	Intermediate Similarity	NPD5760	Phase 2
0.7151	Intermediate Similarity	NPD5761	Phase 2
0.7143	Intermediate Similarity	NPD3972	Approved
0.7135	Intermediate Similarity	NPD7696	Phase 3
0.7135	Intermediate Similarity	NPD7698	Approved
0.7135	Intermediate Similarity	NPD7697	Approved
0.7135	Intermediate Similarity	NPD4287	Approved
0.7134	Intermediate Similarity	NPD3018	Phase 2
0.7134	Intermediate Similarity	NPD2424	Discontinued
0.7115	Intermediate Similarity	NPD3267	Approved
0.7115	Intermediate Similarity	NPD3266	Approved
0.711	Intermediate Similarity	NPD4288	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