NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	228.04
Volume:	224.441
LogP:	2.88
LogD:	2.628
LogS:	-3.393
# Rotatable Bonds:	0
TPSA:	70.67
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.579
Synthetic Accessibility Score:	2.141
Fsp3:	0.0
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:	-4.807
MDCK Permeability:	1.129432439483935e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.415
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.53
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.026
Plasma Protein Binding (PPB):	94.98776245117188%
Volume Distribution (VD):	0.531
Pgp-substrate:	8.68422794342041%

ADMET: Metabolism

CYP1A2-inhibitor:	0.987
CYP1A2-substrate:	0.503
CYP2C19-inhibitor:	0.529
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.564
CYP2C9-substrate:	0.944
CYP2D6-inhibitor:	0.811
CYP2D6-substrate:	0.844
CYP3A4-inhibitor:	0.544
CYP3A4-substrate:	0.162

ADMET: Excretion

Clearance (CL):	4.532
Half-life (T1/2):	0.779

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.127
Drug-inuced Liver Injury (DILI):	0.924
AMES Toxicity:	0.732
Rat Oral Acute Toxicity:	0.133
Maximum Recommended Daily Dose:	0.435
Skin Sensitization:	0.935
Carcinogencity:	0.823
Eye Corrosion:	0.291
Eye Irritation:	0.987
Respiratory Toxicity:	0.22

Download Data

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

Natural Product: NPC9985

Natural Product ID:	NPC9985
*Common Name:**	1,6-Dihydroxyxanthone
IUPAC Name:	1,6-dihydroxyxanthen-9-one
Synonyms:	1,6-Dihydroxyxanthone
Standard InCHIKey:	IUSXGFFUHTXSRD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C13H8O4/c14-7-4-5-8-11(6-7)17-10-3-1-2-9(15)12(10)13(8)16/h1-6,14-15H
SMILES:	Oc1ccc2c(c1)oc1c(c2=O)c(O)ccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL459695
PubChem CID:	5493674
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	roots	n.a.	n.a.	PMID[16989524]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[22863942]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[24042007]
NPO17386	Securidaca longepedunculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24216090]
NPO6714	Securidaca inappendiculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6714	Securidaca inappendiculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6714	Securidaca inappendiculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17386	Securidaca longepedunculata	Species	Polygalaceae	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	5
MIC	6
Others	2

Activity Type	# Activity
Cell Line	4
NON-MOLECULAR	2
Organism	5
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	93000.0	nM	PMID[454340]
NPT15	Cell Line	Jurkat	Homo sapiens	IC50	=	75000.0	nM	PMID[454340]
NPT34	Cell Line	BV-2	Mus musculus	Inhibition	>	80.0	%	PMID[454341]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	18400.0	nM	PMID[454343]
NPT2	Others	Unspecified		IC50	=	131400.0	nM	PMID[454339]
NPT2	Others	Unspecified		IC50	=	7585775.75	nM	PMID[454339]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	32.0	ug.mL-1	PMID[454340]
NPT1118	Organism	Streptococcus pneumoniae	Streptococcus pneumoniae	MIC	>	128.0	ug.mL-1	PMID[454340]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	>	128.0	ug.mL-1	PMID[454340]
NPT1121	Organism	Moraxella catarrhalis	Moraxella catarrhalis	MIC	=	8.0	ug.mL-1	PMID[454340]
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	MIC	>	128.0	ug.mL-1	PMID[454340]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	128.0	ug.mL-1	PMID[454340]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	PC50	>	100.0	uM	PMID[454342]

☑ 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 NPC9985 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	513
0.1-0.2	2200
0.2-0.3	5700
0.3-0.4	12395
0.4-0.5	4358
0.5-0.6	4803
0.6-0.7	5652
0.7-0.8	3977
0.8-0.85	1673
0.85-0.9	1113
0.9-0.95	269
0.95-1	44

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC239495
0.9773	High Similarity	NPC472460
0.9773	High Similarity	NPC147686
0.9773	High Similarity	NPC329225
0.9769	High Similarity	NPC172262
0.9699	High Similarity	NPC261234
0.9697	High Similarity	NPC107586
0.9697	High Similarity	NPC287246
0.9697	High Similarity	NPC296490
0.9697	High Similarity	NPC79943
0.9697	High Similarity	NPC476480
0.9697	High Similarity	NPC275055
0.9697	High Similarity	NPC32441
0.9697	High Similarity	NPC290291
0.9697	High Similarity	NPC13768
0.9697	High Similarity	NPC84585
0.9697	High Similarity	NPC12296
0.9697	High Similarity	NPC295261
0.9697	High Similarity	NPC243083
0.9692	High Similarity	NPC213216
0.9692	High Similarity	NPC274121
0.9692	High Similarity	NPC57601
0.9692	High Similarity	NPC78540
0.9692	High Similarity	NPC50898
0.9627	High Similarity	NPC69769
0.9624	High Similarity	NPC280284
0.9624	High Similarity	NPC188947
0.9624	High Similarity	NPC118813
0.9624	High Similarity	NPC99333
0.9556	High Similarity	NPC3188
0.9552	High Similarity	NPC20709
0.9552	High Similarity	NPC316480
0.9552	High Similarity	NPC225153
0.9552	High Similarity	NPC222342
0.9552	High Similarity	NPC329203
0.9552	High Similarity	NPC150648
0.9552	High Similarity	NPC310135
0.9552	High Similarity	NPC265871
0.9552	High Similarity	NPC274784
0.9549	High Similarity	NPC266597
0.9549	High Similarity	NPC228661
0.9549	High Similarity	NPC299379
0.9549	High Similarity	NPC250266
0.9538	High Similarity	NPC113006
0.9485	High Similarity	NPC169479
0.9485	High Similarity	NPC159855
0.9485	High Similarity	NPC144499
0.9485	High Similarity	NPC202981
0.9481	High Similarity	NPC270883
0.9481	High Similarity	NPC129853
0.9481	High Similarity	NPC188243
0.9481	High Similarity	NPC261227
0.9481	High Similarity	NPC110228
0.9481	High Similarity	NPC284550
0.9481	High Similarity	NPC6407
0.9481	High Similarity	NPC76445
0.9481	High Similarity	NPC172986
0.9478	High Similarity	NPC201395
0.9478	High Similarity	NPC124269
0.9474	High Similarity	NPC29353
0.9474	High Similarity	NPC13408
0.9474	High Similarity	NPC256042
0.9474	High Similarity	NPC124784
0.9474	High Similarity	NPC473887
0.9474	High Similarity	NPC216361
0.9474	High Similarity	NPC194281
0.9474	High Similarity	NPC127447
0.9474	High Similarity	NPC234133
0.9474	High Similarity	NPC116775
0.9474	High Similarity	NPC47815
0.9474	High Similarity	NPC281917
0.9474	High Similarity	NPC187432
0.9474	High Similarity	NPC231772
0.9416	High Similarity	NPC39329
0.9416	High Similarity	NPC310130
0.9416	High Similarity	NPC257097
0.9416	High Similarity	NPC68104
0.9416	High Similarity	NPC169591
0.9416	High Similarity	NPC166138
0.9416	High Similarity	NPC150408
0.9416	High Similarity	NPC143896
0.9416	High Similarity	NPC106985
0.9416	High Similarity	NPC164980
0.9416	High Similarity	NPC221432
0.9416	High Similarity	NPC38219
0.9416	High Similarity	NPC149026
0.9416	High Similarity	NPC91560
0.9416	High Similarity	NPC75049
0.9416	High Similarity	NPC18585
0.9416	High Similarity	NPC175504
0.9412	High Similarity	NPC156590
0.9412	High Similarity	NPC324386
0.9412	High Similarity	NPC312391
0.9412	High Similarity	NPC213322
0.9412	High Similarity	NPC110969
0.9412	High Similarity	NPC205006
0.9412	High Similarity	NPC118840
0.9412	High Similarity	NPC147688
0.9412	High Similarity	NPC64908
0.9412	High Similarity	NPC4743
0.9407	High Similarity	NPC78913
0.9407	High Similarity	NPC55018
0.9407	High Similarity	NPC216978
0.9407	High Similarity	NPC220062
0.9407	High Similarity	NPC301217
0.9407	High Similarity	NPC303633
0.9407	High Similarity	NPC140890
0.9407	High Similarity	NPC18260
0.9407	High Similarity	NPC96565
0.9403	High Similarity	NPC254841
0.9403	High Similarity	NPC188879
0.9398	High Similarity	NPC39426
0.9398	High Similarity	NPC234560
0.9389	High Similarity	NPC313618
0.9348	High Similarity	NPC184649
0.9348	High Similarity	NPC473015
0.9348	High Similarity	NPC236766
0.9348	High Similarity	NPC473013
0.9348	High Similarity	NPC209040
0.9348	High Similarity	NPC197252
0.9348	High Similarity	NPC303185
0.9343	High Similarity	NPC76372
0.9343	High Similarity	NPC161506
0.9343	High Similarity	NPC324436
0.9343	High Similarity	NPC177354
0.9343	High Similarity	NPC182852
0.9343	High Similarity	NPC328164
0.9343	High Similarity	NPC148757
0.9343	High Similarity	NPC166482
0.9343	High Similarity	NPC194432
0.9343	High Similarity	NPC32739
0.9343	High Similarity	NPC226636
0.9343	High Similarity	NPC125855
0.9343	High Similarity	NPC324134
0.9343	High Similarity	NPC296917
0.9343	High Similarity	NPC228504
0.9343	High Similarity	NPC306829
0.9343	High Similarity	NPC220998
0.9343	High Similarity	NPC37496
0.9343	High Similarity	NPC66515
0.9343	High Similarity	NPC40833
0.9343	High Similarity	NPC167624
0.9343	High Similarity	NPC76338
0.9343	High Similarity	NPC107572
0.9343	High Similarity	NPC227579
0.9343	High Similarity	NPC166934
0.9343	High Similarity	NPC223500
0.9343	High Similarity	NPC11561
0.9343	High Similarity	NPC265040
0.9343	High Similarity	NPC1089
0.9343	High Similarity	NPC10937
0.9343	High Similarity	NPC64915
0.9343	High Similarity	NPC78
0.9338	High Similarity	NPC269652
0.9338	High Similarity	NPC182421
0.9338	High Similarity	NPC235239
0.9338	High Similarity	NPC475680
0.9338	High Similarity	NPC159275
0.9338	High Similarity	NPC241100
0.9338	High Similarity	NPC275734
0.9338	High Similarity	NPC305355
0.9338	High Similarity	NPC281207
0.9328	High Similarity	NPC87545
0.9328	High Similarity	NPC240593
0.9328	High Similarity	NPC235428
0.9323	High Similarity	NPC286336
0.9323	High Similarity	NPC248872
0.9318	High Similarity	NPC129132
0.9318	High Similarity	NPC87231
0.9318	High Similarity	NPC212631
0.9318	High Similarity	NPC257756
0.9318	High Similarity	NPC205468
0.9313	High Similarity	NPC137264
0.9313	High Similarity	NPC5515
0.9313	High Similarity	NPC270369
0.9308	High Similarity	NPC197425
0.9281	High Similarity	NPC477955
0.9281	High Similarity	NPC148011
0.9281	High Similarity	NPC1940
0.9281	High Similarity	NPC229190
0.9281	High Similarity	NPC299011
0.9281	High Similarity	NPC196114
0.9275	High Similarity	NPC125894
0.9275	High Similarity	NPC316816
0.9275	High Similarity	NPC219915
0.9275	High Similarity	NPC77794
0.9275	High Similarity	NPC113770
0.9275	High Similarity	NPC107177
0.9275	High Similarity	NPC478086
0.9275	High Similarity	NPC81697
0.9275	High Similarity	NPC185276
0.9275	High Similarity	NPC214166
0.9275	High Similarity	NPC85162
0.9275	High Similarity	NPC223812
0.9275	High Similarity	NPC278249
0.927	High Similarity	NPC96408
0.927	High Similarity	NPC248372
0.927	High Similarity	NPC14871
0.927	High Similarity	NPC282300
0.927	High Similarity	NPC156190

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 NPC9985 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	501
0.1-0.2	997
0.2-0.3	1576
0.3-0.4	2748
0.4-0.5	1822
0.5-0.6	1052
0.6-0.7	284
0.7-0.8	112
0.8-0.85	35
0.85-0.9	15
0.9-0.95	8
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9773	High Similarity	NPD1549	Phase 2
0.9697	High Similarity	NPD1552	Clinical (unspecified phase)
0.9697	High Similarity	NPD1550	Clinical (unspecified phase)
0.9398	High Similarity	NPD1510	Phase 2
0.9389	High Similarity	NPD1240	Approved
0.9248	High Similarity	NPD1607	Approved
0.9071	High Similarity	NPD7410	Clinical (unspecified phase)
0.9071	High Similarity	NPD4378	Clinical (unspecified phase)
0.9	High Similarity	NPD1511	Approved
0.8905	High Similarity	NPD2796	Approved
0.8873	High Similarity	NPD1512	Approved
0.8828	High Similarity	NPD7411	Suspended
0.8786	High Similarity	NPD3750	Approved
0.8767	High Similarity	NPD1934	Approved
0.8759	High Similarity	NPD4380	Phase 2
0.8707	High Similarity	NPD2393	Clinical (unspecified phase)
0.8658	High Similarity	NPD4381	Clinical (unspecified phase)
0.8658	High Similarity	NPD7075	Discontinued
0.8658	High Similarity	NPD3749	Approved
0.8649	High Similarity	NPD8443	Clinical (unspecified phase)
0.8633	High Similarity	NPD1551	Phase 2
0.8601	High Similarity	NPD6799	Approved
0.8581	High Similarity	NPD7096	Clinical (unspecified phase)
0.8581	High Similarity	NPD7819	Suspended
0.8571	High Similarity	NPD1203	Approved
0.8456	Intermediate Similarity	NPD2801	Approved
0.8429	Intermediate Similarity	NPD3748	Approved
0.8409	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.8389	Intermediate Similarity	NPD6801	Discontinued
0.838	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.8378	Intermediate Similarity	NPD6599	Discontinued
0.8344	Intermediate Similarity	NPD3882	Suspended
0.8323	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.8322	Intermediate Similarity	NPD2800	Approved
0.8322	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.8322	Intermediate Similarity	NPD1243	Approved
0.831	Intermediate Similarity	NPD2344	Approved
0.8273	Intermediate Similarity	NPD943	Approved
0.8261	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.8224	Intermediate Similarity	NPD7768	Phase 2
0.8209	Intermediate Similarity	NPD9717	Approved
0.8205	Intermediate Similarity	NPD6166	Phase 2
0.8205	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.8205	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.8176	Intermediate Similarity	NPD5403	Approved
0.8163	Intermediate Similarity	NPD5401	Approved
0.8151	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.8134	Intermediate Similarity	NPD1610	Phase 2
0.8129	Intermediate Similarity	NPD2313	Discontinued
0.8129	Intermediate Similarity	NPD6959	Discontinued
0.8106	Intermediate Similarity	NPD1548	Phase 1
0.8105	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8101	Intermediate Similarity	NPD3818	Discontinued
0.8082	Intermediate Similarity	NPD2309	Approved
0.8054	Intermediate Similarity	NPD920	Approved
0.805	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.8042	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.8042	Intermediate Similarity	NPD2799	Discontinued
0.8041	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.8039	Intermediate Similarity	NPD3817	Phase 2
0.8028	Intermediate Similarity	NPD6651	Approved
0.8014	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD422	Phase 1
0.8	Intermediate Similarity	NPD7074	Phase 3
0.7986	Intermediate Similarity	NPD6099	Approved
0.7986	Intermediate Similarity	NPD6100	Approved
0.7986	Intermediate Similarity	NPD2935	Discontinued
0.7974	Intermediate Similarity	NPD1465	Phase 2
0.7949	Intermediate Similarity	NPD5494	Approved
0.7937	Intermediate Similarity	NPD7054	Approved
0.7888	Intermediate Similarity	NPD7472	Approved
0.7872	Intermediate Similarity	NPD3268	Approved
0.7857	Intermediate Similarity	NPD4908	Phase 1
0.7857	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7857	Intermediate Similarity	NPD6832	Phase 2
0.7842	Intermediate Similarity	NPD2798	Approved
0.784	Intermediate Similarity	NPD6797	Phase 2
0.784	Intermediate Similarity	NPD5953	Discontinued
0.7829	Intermediate Similarity	NPD3226	Approved
0.7826	Intermediate Similarity	NPD7286	Phase 2
0.7826	Intermediate Similarity	NPD3225	Approved
0.7808	Intermediate Similarity	NPD2346	Discontinued
0.7806	Intermediate Similarity	NPD5402	Approved
0.7793	Intermediate Similarity	NPD4308	Phase 3
0.7791	Intermediate Similarity	NPD7251	Discontinued
0.7791	Intermediate Similarity	NPD6559	Discontinued
0.7786	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.777	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.777	Intermediate Similarity	NPD2797	Approved
0.777	Intermediate Similarity	NPD4628	Phase 3
0.7746	Intermediate Similarity	NPD1296	Phase 2
0.7746	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7744	Intermediate Similarity	NPD7808	Phase 3
0.7744	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7744	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7736	Intermediate Similarity	NPD6232	Discontinued
0.7708	Intermediate Similarity	NPD1933	Approved
0.7704	Intermediate Similarity	NPD9545	Approved
0.7702	Intermediate Similarity	NPD7473	Discontinued
0.7692	Intermediate Similarity	NPD4288	Approved
0.7687	Intermediate Similarity	NPD9493	Approved
0.7682	Intermediate Similarity	NPD2534	Approved
0.7682	Intermediate Similarity	NPD2532	Approved
0.7682	Intermediate Similarity	NPD2533	Approved
0.7681	Intermediate Similarity	NPD1608	Approved
0.7671	Intermediate Similarity	NPD7033	Discontinued
0.7658	Intermediate Similarity	NPD919	Approved
0.7643	Intermediate Similarity	NPD3266	Approved
0.7643	Intermediate Similarity	NPD1470	Approved
0.7643	Intermediate Similarity	NPD3267	Approved
0.7639	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7639	Intermediate Similarity	NPD1613	Approved
0.7622	Intermediate Similarity	NPD3764	Approved
0.7622	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7622	Intermediate Similarity	NPD411	Approved
0.7609	Intermediate Similarity	NPD1201	Approved
0.7607	Intermediate Similarity	NPD5844	Phase 1
0.7594	Intermediate Similarity	NPD1241	Discontinued
0.7586	Intermediate Similarity	NPD447	Suspended
0.7584	Intermediate Similarity	NPD2654	Approved
0.7578	Intermediate Similarity	NPD3926	Phase 2
0.7574	Intermediate Similarity	NPD4287	Approved
0.7562	Intermediate Similarity	NPD1247	Approved
0.7554	Intermediate Similarity	NPD3972	Approved
0.7554	Intermediate Similarity	NPD1481	Phase 2
0.7551	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7518	Intermediate Similarity	NPD1164	Approved
0.7517	Intermediate Similarity	NPD4307	Phase 2
0.75	Intermediate Similarity	NPD7390	Discontinued
0.7482	Intermediate Similarity	NPD1535	Discovery
0.7468	Intermediate Similarity	NPD2296	Approved
0.7468	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7466	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7466	Intermediate Similarity	NPD230	Phase 1
0.7465	Intermediate Similarity	NPD1019	Discontinued
0.7464	Intermediate Similarity	NPD17	Approved
0.7455	Intermediate Similarity	NPD1729	Discontinued
0.7451	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.745	Intermediate Similarity	NPD1471	Phase 3
0.7431	Intermediate Similarity	NPD4625	Phase 3
0.7399	Intermediate Similarity	NPD4360	Phase 2
0.7399	Intermediate Similarity	NPD4363	Phase 3
0.7389	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7376	Intermediate Similarity	NPD4749	Approved
0.7368	Intermediate Similarity	NPD2354	Approved
0.7365	Intermediate Similarity	NPD6104	Discontinued
0.7348	Intermediate Similarity	NPD74	Approved
0.7348	Intermediate Similarity	NPD9266	Approved
0.7347	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.7347	Intermediate Similarity	NPD5124	Phase 1
0.7333	Intermediate Similarity	NPD3751	Discontinued
0.7314	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD9263	Approved
0.7273	Intermediate Similarity	NPD9267	Approved
0.7273	Intermediate Similarity	NPD9265	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD9264	Approved
0.7267	Intermediate Similarity	NPD5405	Approved
0.7267	Intermediate Similarity	NPD5406	Approved
0.7267	Intermediate Similarity	NPD5404	Approved
0.7267	Intermediate Similarity	NPD5408	Approved
0.7261	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.726	Intermediate Similarity	NPD6798	Discontinued
0.7257	Intermediate Similarity	NPD4362	Clinical (unspecified phase)
0.7257	Intermediate Similarity	NPD4361	Phase 2
0.7241	Intermediate Similarity	NPD1008	Clinical (unspecified phase)
0.7229	Intermediate Similarity	NPD5940	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD2355	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD2353	Approved
0.7215	Intermediate Similarity	NPD6585	Discontinued
0.7203	Intermediate Similarity	NPD1876	Approved
0.7195	Intermediate Similarity	NPD5710	Approved
0.7195	Intermediate Similarity	NPD5711	Approved
0.7194	Intermediate Similarity	NPD1894	Discontinued
0.7191	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7174	Intermediate Similarity	NPD405	Clinical (unspecified phase)
0.7172	Intermediate Similarity	NPD2861	Phase 2
0.717	Intermediate Similarity	NPD5889	Approved
0.717	Intermediate Similarity	NPD5890	Approved
0.7162	Intermediate Similarity	NPD3140	Approved
0.7162	Intermediate Similarity	NPD3142	Approved
0.7161	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD7458	Discontinued
0.7125	Intermediate Similarity	NPD7577	Discontinued
0.7125	Intermediate Similarity	NPD6844	Discontinued
0.7124	Intermediate Similarity	NPD1652	Phase 2
0.7115	Intermediate Similarity	NPD4662	Approved
0.7115	Intermediate Similarity	NPD4661	Approved
0.7108	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7105	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7097	Intermediate Similarity	NPD7440	Discontinued
0.7091	Intermediate Similarity	NPD3787	Discontinued
0.7086	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7078	Intermediate Similarity	NPD7003	Approved
0.7076	Intermediate Similarity	NPD8313	Approved
0.7076	Intermediate Similarity	NPD8312	Approved
0.707	Intermediate Similarity	NPD5049	Phase 3
0.7063	Intermediate Similarity	NPD9269	Phase 2
0.7055	Intermediate Similarity	NPD6971	Discontinued
0.7055	Intermediate Similarity	NPD9494	Approved
0.7051	Intermediate Similarity	NPD7212	Phase 2

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