NPASS Compound

Structure

NPC476433 OpenBabel07101719252D 31 34 0 0 1 0 0 0 0 0999 V2000 4.2359 -4.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9679 -7.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4320 -5.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9320 -5.9670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8339 -4.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8804 -4.7169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5660 -3.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9679 -4.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7000 -7.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9679 -5.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5660 -6.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1019 -2.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4320 -4.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7000 -4.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2359 -2.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.7784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2653 -3.5955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1019 -3.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8339 -6.6009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8339 -5.6009 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 8.5660 -5.6009 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.4563 -2.1942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1473 -1.2431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7872 -2.9373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4320 -5.1009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7000 -5.1009 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.8164 -0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.1691 -1.0352 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 -2.7294 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2872 -3.8034 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 3.3698 -2.6009 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 19 2 0 0 0 0 3 25 1 0 0 0 0 4 25 1 0 0 0 0 5 26 1 0 0 0 0 6 30 1 0 0 0 0 7 13 1 0 0 0 0 7 14 1 0 0 0 0 8 10 1 0 0 0 0 8 18 1 0 0 0 0 9 11 1 0 0 0 0 9 19 1 0 0 0 0 10 20 1 0 0 0 0 11 21 1 0 0 0 0 12 15 1 0 0 0 0 12 18 2 0 0 0 0 13 25 1 0 0 0 0 14 26 1 0 0 0 0 15 31 1 0 0 0 0 16 28 2 0 0 0 0 16 29 1 0 0 0 0 17 30 2 0 0 0 0 17 31 1 0 0 0 0 19 20 1 0 0 0 0 20 26 1 0 0 0 0 21 25 1 0 0 0 0 21 26 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 22 31 1 0 0 0 0 23 27 1 0 0 0 0 23 28 1 0 0 0 0 24 29 2 0 0 0 0 24 30 1 0 0 0 0 M CHG 1 30 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	422.33
Volume:	464.51
LogP:	4.0
LogD:	5.273
LogS:	-3.094
# Rotatable Bonds:	5
TPSA:	61.34
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.505
Synthetic Accessibility Score:	4.814
Fsp3:	0.654
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.443
MDCK Permeability:	2.9810485102643725e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.487
20% Bioavailability (F20%):	0.984
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.209
Plasma Protein Binding (PPB):	66.41240692138672%
Volume Distribution (VD):	1.095
Pgp-substrate:	40.528804779052734%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.114
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.028
CYP2C9-substrate:	0.216
CYP2D6-inhibitor:	0.962
CYP2D6-substrate:	0.365
CYP3A4-inhibitor:	0.149
CYP3A4-substrate:	0.24

ADMET: Excretion

Clearance (CL):	5.636
Half-life (T1/2):	0.819

ADMET: Toxicity

hERG Blockers:	0.138
Human Hepatotoxicity (H-HT):	0.843
Drug-inuced Liver Injury (DILI):	0.119
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.669
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.059
Carcinogencity:	0.032
Eye Corrosion:	0.003
Eye Irritation:	0.05
Respiratory Toxicity:	0.773

Download Data

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

Natural Product: NPC476433

Natural Product ID:	NPC476433
*Common Name:**	Agelasine D
IUPAC Name:	7-[(E)-5-[(1R,4aR,8aR)-5,5,8a-trimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]-3-methylpent-2-enyl]-9-methylpurin-9-ium-6-amine;chloride
Synonyms:	Agelasine D
Standard InCHIKey:	VKMLEXNPDUMVEC-ZHZNLTMTSA-M
Standard InCHI:	InChI=1S/C26H40N5.ClH/c1-18(12-15-31-17-30(6)24-22(31)23(27)28-16-29-24)8-10-20-19(2)9-11-21-25(3,4)13-7-14-26(20,21)5;/h12,16-17,20-21H,2,7-11,13-15H2,1,3-6H3,(H2,27,28,29);1H/q+1;/p-1/b18-12+;/t20-,21-,26+;/m1./s1
SMILES:	CC(=CCN1C=[N+](C2=NC=NC(=C21)N)C)CCC3C(=C)CCC4C3(CCCC4(C)C)C.[Cl-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL604730
PubChem CID:	46231918
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	at a depth of 14 m near the island of Ambon (Seram Seilale), Indonesia	1997-AUG	PMID[10514317]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[14677933]
NPO33334	agelas sponges	Species	Agelasidae	Eukaryota	n.a.	Indonesian	n.a.	PMID[20061160]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[26083682]
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	papua new guinean	n.a.	PMID[9784179]
NPO11199	Agelas nakamurai	Species	Agelasidae	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	4
MIC	2
Others	3

Activity Type	# Activity
Cell Line	2
Individual Protein	1
NON-MOLECULAR	2
Organism	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1864	Cell Line	L5178Y	Mus musculus	GI	=	1.9	%	PMID[531475]
NPT1864	Cell Line	L5178Y	Mus musculus	IC50	=	4030.0	nM	PMID[531475]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	>	24000.0	nM	PMID[531477]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	<	87.7	nM	PMID[531475]
NPT471	Organism	Trypanosoma brucei brucei	Trypanosoma brucei brucei	MIC	=	14800.0	nM	PMID[531476]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	IZ	=	18.0	mm	PMID[531477]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	IZ	=	14.0	mm	PMID[531477]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	36000.0	nM	PMID[531477]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	19000.0	nM	PMID[531477]

☑ 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 NPC476433 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	889
0.1-0.2	17499
0.2-0.3	18650
0.3-0.4	3576
0.4-0.5	1719
0.5-0.6	309
0.6-0.7	30
0.7-0.8	7
0.8-0.85	3
0.85-0.9	4
0.9-0.95	3
0.95-1	8

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC476528
0.9773	High Similarity	NPC476522
0.9773	High Similarity	NPC476013
0.9773	High Similarity	NPC474986
0.9769	High Similarity	NPC296437
0.9701	High Similarity	NPC476408
0.9699	High Similarity	NPC476521
0.9695	High Similarity	NPC470266
0.9624	High Similarity	NPC476520
0.9065	High Similarity	NPC244700
0.8836	High Similarity	NPC18308
0.8836	High Similarity	NPC472832
0.8819	High Similarity	NPC472834
0.8759	High Similarity	NPC472833
0.8511	High Similarity	NPC217656
0.8194	Intermediate Similarity	NPC89139
0.8012	Intermediate Similarity	NPC473585
0.7818	Intermediate Similarity	NPC265111
0.7154	Intermediate Similarity	NPC174114
0.7154	Intermediate Similarity	NPC87981
0.6974	Remote Similarity	NPC167285
0.6923	Remote Similarity	NPC317054
0.6863	Remote Similarity	NPC226184
0.6863	Remote Similarity	NPC76544
0.6846	Remote Similarity	NPC57279
0.6686	Remote Similarity	NPC164845
0.6618	Remote Similarity	NPC476564
0.6618	Remote Similarity	NPC18335
0.649	Remote Similarity	NPC104011
0.6458	Remote Similarity	NPC68938
0.641	Remote Similarity	NPC33996
0.6383	Remote Similarity	NPC4837
0.6383	Remote Similarity	NPC312187
0.6369	Remote Similarity	NPC129756
0.6347	Remote Similarity	NPC239737
0.6226	Remote Similarity	NPC317821
0.6182	Remote Similarity	NPC150853
0.6175	Remote Similarity	NPC313514
0.6169	Remote Similarity	NPC246193
0.6158	Remote Similarity	NPC313897
0.6154	Remote Similarity	NPC93365
0.6154	Remote Similarity	NPC476219
0.6126	Remote Similarity	NPC469308
0.6125	Remote Similarity	NPC209525
0.6125	Remote Similarity	NPC161659
0.6122	Remote Similarity	NPC189314
0.6089	Remote Similarity	NPC477119
0.6059	Remote Similarity	NPC476297
0.6049	Remote Similarity	NPC314152
0.6049	Remote Similarity	NPC229974
0.6047	Remote Similarity	NPC300238
0.6037	Remote Similarity	NPC189068
0.6036	Remote Similarity	NPC469975
0.6	Remote Similarity	NPC219313
0.6	Remote Similarity	NPC309832
0.5977	Remote Similarity	NPC470203
0.5976	Remote Similarity	NPC107374
0.5976	Remote Similarity	NPC156461
0.5976	Remote Similarity	NPC21448
0.5952	Remote Similarity	NPC114209
0.5948	Remote Similarity	NPC248007
0.5939	Remote Similarity	NPC164665
0.5928	Remote Similarity	NPC136349
0.592	Remote Similarity	NPC470204
0.5904	Remote Similarity	NPC269827
0.5892	Remote Similarity	NPC477118
0.5872	Remote Similarity	NPC120070
0.5868	Remote Similarity	NPC121222
0.586	Remote Similarity	NPC477120
0.5858	Remote Similarity	NPC161224
0.5856	Remote Similarity	NPC189261
0.5838	Remote Similarity	NPC195140
0.5824	Remote Similarity	NPC328479
0.5822	Remote Similarity	NPC158055
0.5804	Remote Similarity	NPC476099
0.5789	Remote Similarity	NPC302778
0.5789	Remote Similarity	NPC212551
0.5765	Remote Similarity	NPC185991
0.5765	Remote Similarity	NPC85689
0.5765	Remote Similarity	NPC211025
0.5758	Remote Similarity	NPC8590
0.5756	Remote Similarity	NPC174802
0.5752	Remote Similarity	NPC139776
0.5739	Remote Similarity	NPC122141
0.5731	Remote Similarity	NPC472816
0.5731	Remote Similarity	NPC321814
0.5728	Remote Similarity	NPC250178
0.5723	Remote Similarity	NPC224076
0.5714	Remote Similarity	NPC276373
0.5706	Remote Similarity	NPC225018
0.5698	Remote Similarity	NPC130586
0.5698	Remote Similarity	NPC164952
0.5696	Remote Similarity	NPC14330
0.569	Remote Similarity	NPC226245
0.5685	Remote Similarity	NPC5802
0.5674	Remote Similarity	NPC317105
0.5668	Remote Similarity	NPC24589
0.5667	Remote Similarity	NPC290959
0.5665	Remote Similarity	NPC471603
0.5664	Remote Similarity	NPC476561
0.566	Remote Similarity	NPC287876
0.5657	Remote Similarity	NPC157821
0.564	Remote Similarity	NPC207633
0.5634	Remote Similarity	NPC115595
0.5632	Remote Similarity	NPC325903
0.5607	Remote Similarity	NPC40070
0.5607	Remote Similarity	NPC160666
0.56	Remote Similarity	NPC316618

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 NPC476433 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	371
0.1-0.2	1107
0.2-0.3	3198
0.3-0.4	2201
0.4-0.5	1559
0.5-0.6	640
0.6-0.7	74
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7379	Intermediate Similarity	NPD1058	Discontinued
0.7073	Intermediate Similarity	NPD1313	Approved
0.6788	Remote Similarity	NPD6074	Clinical (unspecified phase)
0.6766	Remote Similarity	NPD1333	Phase 3
0.6706	Remote Similarity	NPD1567	Clinical (unspecified phase)
0.6705	Remote Similarity	NPD2930	Clinical (unspecified phase)
0.6689	Remote Similarity	NPD870	Clinical (unspecified phase)
0.6688	Remote Similarity	NPD7158	Phase 1
0.6687	Remote Similarity	NPD2593	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD5962	Phase 2
0.6667	Remote Similarity	NPD3378	Clinical (unspecified phase)
0.6648	Remote Similarity	NPD7023	Clinical (unspecified phase)
0.6647	Remote Similarity	NPD1015	Phase 2
0.6647	Remote Similarity	NPD2875	Clinical (unspecified phase)
0.6647	Remote Similarity	NPD1016	Phase 2
0.6627	Remote Similarity	NPD516	Clinical (unspecified phase)
0.6618	Remote Similarity	NPD8836	Approved
0.6609	Remote Similarity	NPD3341	Clinical (unspecified phase)
0.6606	Remote Similarity	NPD2927	Phase 3
0.6554	Remote Similarity	NPD9408	Phase 3
0.6538	Remote Similarity	NPD3485	Clinical (unspecified phase)
0.6534	Remote Similarity	NPD4649	Clinical (unspecified phase)
0.6533	Remote Similarity	NPD9633	Phase 3
0.6529	Remote Similarity	NPD1215	Discontinued
0.6524	Remote Similarity	NPD6129	Phase 2
0.6519	Remote Similarity	NPD4240	Approved
0.6519	Remote Similarity	NPD3419	Clinical (unspecified phase)
0.6505	Remote Similarity	NPD6816	Phase 3
0.6491	Remote Similarity	NPD2333	Discontinued
0.649	Remote Similarity	NPD248	Discontinued
0.6471	Remote Similarity	NPD5269	Clinical (unspecified phase)
0.6461	Remote Similarity	NPD2457	Phase 2
0.6461	Remote Similarity	NPD2456	Phase 2
0.6457	Remote Similarity	NPD7111	Discontinued
0.6455	Remote Similarity	NPD2965	Clinical (unspecified phase)
0.6437	Remote Similarity	NPD3799	Suspended
0.6433	Remote Similarity	NPD6794	Approved
0.6429	Remote Similarity	NPD6761	Discontinued
0.642	Remote Similarity	NPD5730	Phase 2
0.642	Remote Similarity	NPD40	Phase 2
0.641	Remote Similarity	NPD799	Phase 1
0.6393	Remote Similarity	NPD7722	Suspended
0.6392	Remote Similarity	NPD4352	Phase 1
0.6389	Remote Similarity	NPD2793	Discontinued
0.6389	Remote Similarity	NPD4902	Discontinued
0.6384	Remote Similarity	NPD5508	Phase 1
0.638	Remote Similarity	NPD4568	Phase 2
0.6374	Remote Similarity	NPD8120	Approved
0.6374	Remote Similarity	NPD8121	Phase 3
0.6369	Remote Similarity	NPD5463	Clinical (unspecified phase)
0.6344	Remote Similarity	NPD5462	Discontinued
0.6343	Remote Similarity	NPD7006	Approved
0.6337	Remote Similarity	NPD2647	Phase 3
0.6335	Remote Similarity	NPD7323	Phase 2
0.6329	Remote Similarity	NPD3696	Approved
0.6329	Remote Similarity	NPD3695	Approved
0.6325	Remote Similarity	NPD2524	Discontinued
0.6323	Remote Similarity	NPD4763	Clinical (unspecified phase)
0.6304	Remote Similarity	NPD3431	Approved
0.6304	Remote Similarity	NPD6619	Phase 3
0.6304	Remote Similarity	NPD3430	Approved
0.6298	Remote Similarity	NPD2591	Phase 2
0.6298	Remote Similarity	NPD6721	Phase 1
0.6286	Remote Similarity	NPD5324	Clinical (unspecified phase)
0.6273	Remote Similarity	NPD171	Discontinued
0.6272	Remote Similarity	NPD5300	Clinical (unspecified phase)
0.6271	Remote Similarity	NPD3041	Approved
0.6257	Remote Similarity	NPD2526	Phase 2
0.6257	Remote Similarity	NPD1637	Clinical (unspecified phase)
0.6257	Remote Similarity	NPD2523	Phase 2
0.6257	Remote Similarity	NPD5806	Clinical (unspecified phase)
0.625	Remote Similarity	NPD5969	Clinical (unspecified phase)
0.6243	Remote Similarity	NPD2478	Clinical (unspecified phase)
0.6236	Remote Similarity	NPD1892	Phase 2
0.6236	Remote Similarity	NPD3409	Phase 1
0.6236	Remote Similarity	NPD1893	Phase 2
0.6229	Remote Similarity	NPD6828	Phase 2
0.6229	Remote Similarity	NPD6827	Clinical (unspecified phase)
0.6223	Remote Similarity	NPD6468	Clinical (unspecified phase)
0.6223	Remote Similarity	NPD6469	Phase 3
0.6218	Remote Similarity	NPD7445	Phase 1
0.6218	Remote Similarity	NPD2450	Phase 2
0.6218	Remote Similarity	NPD2452	Phase 2
0.6218	Remote Similarity	NPD2453	Phase 2
0.6218	Remote Similarity	NPD2451	Phase 2
0.6216	Remote Similarity	NPD6577	Clinical (unspecified phase)
0.6216	Remote Similarity	NPD4615	Phase 2
0.6216	Remote Similarity	NPD2839	Phase 2
0.6215	Remote Similarity	NPD5843	Discontinued
0.6215	Remote Similarity	NPD2406	Clinical (unspecified phase)
0.6205	Remote Similarity	NPD6192	Phase 3
0.6198	Remote Similarity	NPD5012	Phase 2
0.6186	Remote Similarity	NPD4612	Discontinued
0.6185	Remote Similarity	NPD3889	Approved
0.6175	Remote Similarity	NPD7138	Phase 2
0.6168	Remote Similarity	NPD3107	Discontinued
0.6166	Remote Similarity	NPD2877	Clinical (unspecified phase)
0.6166	Remote Similarity	NPD2876	Phase 3
0.6159	Remote Similarity	NPD4183	Phase 3
0.6159	Remote Similarity	NPD4182	Phase 3
0.6158	Remote Similarity	NPD7297	Phase 2
0.6158	Remote Similarity	NPD6849	Phase 2
0.6158	Remote Similarity	NPD6850	Phase 2
0.6154	Remote Similarity	NPD2646	Discontinued
0.6154	Remote Similarity	NPD546	Clinical (unspecified phase)
0.6133	Remote Similarity	NPD306	Approved
0.6133	Remote Similarity	NPD4441	Phase 2
0.6131	Remote Similarity	NPD1257	Approved
0.6126	Remote Similarity	NPD6151	Phase 2
0.6126	Remote Similarity	NPD4318	Clinical (unspecified phase)
0.6125	Remote Similarity	NPD193	Suspended
0.6122	Remote Similarity	NPD8831	Approved
0.6122	Remote Similarity	NPD8833	Approved
0.612	Remote Similarity	NPD5642	Approved
0.612	Remote Similarity	NPD5682	Phase 3
0.612	Remote Similarity	NPD5683	Clinical (unspecified phase)
0.612	Remote Similarity	NPD5684	Clinical (unspecified phase)
0.6117	Remote Similarity	NPD3362	Clinical (unspecified phase)
0.6111	Remote Similarity	NPD174	Discontinued
0.6108	Remote Similarity	NPD2818	Discontinued
0.6108	Remote Similarity	NPD5145	Clinical (unspecified phase)
0.6105	Remote Similarity	NPD1288	Clinical (unspecified phase)
0.6103	Remote Similarity	NPD2824	Phase 2
0.6103	Remote Similarity	NPD6520	Phase 3
0.6103	Remote Similarity	NPD6521	Phase 3
0.6102	Remote Similarity	NPD5996	Clinical (unspecified phase)
0.6092	Remote Similarity	NPD509	Phase 3
0.6091	Remote Similarity	NPD4863	Approved
0.6087	Remote Similarity	NPD6418	Phase 1
0.6084	Remote Similarity	NPD3708	Phase 2
0.6071	Remote Similarity	NPD3860	Discontinued
0.6071	Remote Similarity	NPD1029	Clinical (unspecified phase)
0.6071	Remote Similarity	NPD1030	Approved
0.6071	Remote Similarity	NPD1027	Approved
0.6062	Remote Similarity	NPD2364	Suspended
0.6059	Remote Similarity	NPD4854	Phase 3
0.6054	Remote Similarity	NPD7504	Discontinued
0.6053	Remote Similarity	NPD5885	Approved
0.6051	Remote Similarity	NPD3905	Phase 3
0.6049	Remote Similarity	NPD185	Approved
0.6042	Remote Similarity	NPD4142	Discontinued
0.6036	Remote Similarity	NPD3612	Phase 2
0.6033	Remote Similarity	NPD2963	Phase 1
0.6032	Remote Similarity	NPD2960	Clinical (unspecified phase)
0.6024	Remote Similarity	NPD1690	Clinical (unspecified phase)
0.6022	Remote Similarity	NPD4716	Approved
0.6022	Remote Similarity	NPD1873	Clinical (unspecified phase)
0.6022	Remote Similarity	NPD702	Clinical (unspecified phase)
0.6019	Remote Similarity	NPD6352	Phase 2
0.601	Remote Similarity	NPD5486	Discontinued
0.6	Remote Similarity	NPD2880	Discontinued
0.6	Remote Similarity	NPD1303	Phase 1
0.6	Remote Similarity	NPD4023	Clinical (unspecified phase)
0.6	Remote Similarity	NPD3002	Clinical (unspecified phase)
0.6	Remote Similarity	NPD1272	Clinical (unspecified phase)
0.6	Remote Similarity	NPD2731	Phase 2
0.6	Remote Similarity	NPD7988	Suspended
0.6	Remote Similarity	NPD1807	Clinical (unspecified phase)
0.6	Remote Similarity	NPD6271	Approved
0.599	Remote Similarity	NPD6470	Phase 3
0.5989	Remote Similarity	NPD1895	Discontinued
0.5989	Remote Similarity	NPD7709	Discontinued
0.5989	Remote Similarity	NPD4744	Clinical (unspecified phase)
0.5989	Remote Similarity	NPD1674	Clinical (unspecified phase)
0.5989	Remote Similarity	NPD1675	Phase 1
0.598	Remote Similarity	NPD2903	Clinical (unspecified phase)
0.598	Remote Similarity	NPD7164	Discontinued
0.598	Remote Similarity	NPD2902	Phase 2
0.5978	Remote Similarity	NPD2868	Clinical (unspecified phase)
0.5978	Remote Similarity	NPD4298	Clinical (unspecified phase)
0.5976	Remote Similarity	NPD250	Approved
0.5976	Remote Similarity	NPD166	Approved
0.5976	Remote Similarity	NPD249	Approved
0.5972	Remote Similarity	NPD7502	Clinical (unspecified phase)
0.5968	Remote Similarity	NPD2728	Approved
0.5968	Remote Similarity	NPD2729	Approved
0.5968	Remote Similarity	NPD2730	Approved
0.5967	Remote Similarity	NPD3432	Approved
0.5966	Remote Similarity	NPD4213	Clinical (unspecified phase)
0.5966	Remote Similarity	NPD3361	Phase 1
0.5965	Remote Similarity	NPD3405	Phase 3
0.596	Remote Similarity	NPD4990	Clinical (unspecified phase)
0.5949	Remote Similarity	NPD7103	Approved
0.5948	Remote Similarity	NPD9084	Phase 2
0.5947	Remote Similarity	NPD7935	Phase 2
0.5946	Remote Similarity	NPD5757	Discontinued
0.5944	Remote Similarity	NPD5943	Clinical (unspecified phase)
0.5941	Remote Similarity	NPD2128	Phase 1
0.593	Remote Similarity	NPD2150	Discontinued
0.593	Remote Similarity	NPD3265	Phase 1
0.5928	Remote Similarity	NPD2881	Approved
0.5928	Remote Similarity	NPD2807	Discontinued
0.5928	Remote Similarity	NPD548	Clinical (unspecified phase)
0.5928	Remote Similarity	NPD2879	Approved
0.5918	Remote Similarity	NPD5458	Discontinued
0.5916	Remote Similarity	NPD3830	Phase 1
0.5915	Remote Similarity	NPD3706	Clinical (unspecified phase)
0.5914	Remote Similarity	NPD7394	Phase 2
0.5912	Remote Similarity	NPD4155	Approved
0.5912	Remote Similarity	NPD9484	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