NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	256.08
Volume:	254.94
LogP:	2.475
LogD:	2.494
LogS:	-3.425
# Rotatable Bonds:	3
TPSA:	64.21
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.715
Synthetic Accessibility Score:	2.212
Fsp3:	0.143
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:	-4.951
MDCK Permeability:	1.5235377759381663e-05
Pgp-inhibitor:	0.028
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.101

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.947
Plasma Protein Binding (PPB):	84.1748046875%
Volume Distribution (VD):	0.88
Pgp-substrate:	13.772268295288086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.99
CYP1A2-substrate:	0.962
CYP2C19-inhibitor:	0.824
CYP2C19-substrate:	0.465
CYP2C9-inhibitor:	0.357
CYP2C9-substrate:	0.925
CYP2D6-inhibitor:	0.766
CYP2D6-substrate:	0.879
CYP3A4-inhibitor:	0.833
CYP3A4-substrate:	0.203

ADMET: Excretion

Clearance (CL):	6.471
Half-life (T1/2):	0.495

ADMET: Toxicity

hERG Blockers:	0.065
Human Hepatotoxicity (H-HT):	0.834
Drug-inuced Liver Injury (DILI):	0.955
AMES Toxicity:	0.774
Rat Oral Acute Toxicity:	0.803
Maximum Recommended Daily Dose:	0.904
Skin Sensitization:	0.539
Carcinogencity:	0.142
Eye Corrosion:	0.009
Eye Irritation:	0.905
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC260434

Natural Product ID:	NPC260434
*Common Name:**	Harmic Acid Methyl Ester
IUPAC Name:	methyl 7-methoxy-9H-pyrido[3,4-b]indole-1-carboxylate
Synonyms:	Harmic Acid Methyl Ester
Standard InCHIKey:	GGTFWDPYRXONGD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C14H12N2O3/c1-18-8-3-4-9-10-5-6-15-13(14(17)19-2)12(10)16-11(9)7-8/h3-7,16H,1-2H3
SMILES:	COc1ccc2c(c1)[nH]c1c2ccnc1C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1957116
PubChem CID:	57391302
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001140] Harmala alkaloids

*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
NPO503	Trigonostemon lii	Species	Euphorbiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[22342628]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[28128938]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6736972]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1085	Peganum harmala	Species	Nitrariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO503	Trigonostemon lii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1085	Peganum harmala	Species	Nitrariaceae	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	8

Activity Type	# Activity
Cell Line	8

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	40000.0	nM	PMID[551789]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	>	40000.0	nM	PMID[551789]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	40000.0	nM	PMID[551789]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[551789]
NPT660	Cell Line	SW480	Homo sapiens	IC50	>	40000.0	nM	PMID[551789]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[551790]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	>	10000.0	nM	PMID[551790]
NPT515	Cell Line	SGC-7901	Homo sapiens	IC50	>	10000.0	nM	PMID[551790]

☑ 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 NPC260434 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	596
0.1-0.2	4258
0.2-0.3	12738
0.3-0.4	7859
0.4-0.5	12363
0.5-0.6	2246
0.6-0.7	1989
0.7-0.8	580
0.8-0.85	49
0.85-0.9	15
0.9-0.95	2
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.961	High Similarity	NPC122436
0.912	High Similarity	NPC235685
0.9078	High Similarity	NPC101350
0.902	High Similarity	NPC266249
0.8957	High Similarity	NPC60621
0.8932	High Similarity	NPC123839
0.8853	High Similarity	NPC182222
0.8824	High Similarity	NPC148889
0.8756	High Similarity	NPC63971
0.8756	High Similarity	NPC91868
0.8756	High Similarity	NPC118940
0.8725	High Similarity	NPC232727
0.851	High Similarity	NPC132539
0.8448	Intermediate Similarity	NPC53534
0.8412	Intermediate Similarity	NPC258048
0.8406	Intermediate Similarity	NPC19872
0.8396	Intermediate Similarity	NPC167860
0.8396	Intermediate Similarity	NPC123976
0.8364	Intermediate Similarity	NPC476287
0.8312	Intermediate Similarity	NPC152620
0.8303	Intermediate Similarity	NPC323969
0.8286	Intermediate Similarity	NPC476138
0.8286	Intermediate Similarity	NPC245816
0.8263	Intermediate Similarity	NPC174758
0.8255	Intermediate Similarity	NPC4687
0.8249	Intermediate Similarity	NPC27041
0.823	Intermediate Similarity	NPC176538
0.8206	Intermediate Similarity	NPC471762
0.8178	Intermediate Similarity	NPC185782
0.8174	Intermediate Similarity	NPC213530
0.8174	Intermediate Similarity	NPC193267
0.816	Intermediate Similarity	NPC285558
0.8157	Intermediate Similarity	NPC477979
0.8125	Intermediate Similarity	NPC194740
0.8108	Intermediate Similarity	NPC229893
0.8102	Intermediate Similarity	NPC87413
0.8097	Intermediate Similarity	NPC196718
0.8097	Intermediate Similarity	NPC102593
0.8077	Intermediate Similarity	NPC165964
0.8065	Intermediate Similarity	NPC26679
0.8045	Intermediate Similarity	NPC473041
0.8044	Intermediate Similarity	NPC66777
0.8037	Intermediate Similarity	NPC36405
0.8037	Intermediate Similarity	NPC274982
0.8035	Intermediate Similarity	NPC15801
0.8028	Intermediate Similarity	NPC89508
0.8026	Intermediate Similarity	NPC178858
0.8009	Intermediate Similarity	NPC174672
0.8	Intermediate Similarity	NPC183777
0.8	Intermediate Similarity	NPC249583
0.8	Intermediate Similarity	NPC305984
0.8	Intermediate Similarity	NPC267928
0.7991	Intermediate Similarity	NPC116238
0.7981	Intermediate Similarity	NPC57398
0.7963	Intermediate Similarity	NPC287208
0.7955	Intermediate Similarity	NPC152768
0.7955	Intermediate Similarity	NPC8022
0.7955	Intermediate Similarity	NPC148183
0.7955	Intermediate Similarity	NPC470799
0.7944	Intermediate Similarity	NPC165599
0.7939	Intermediate Similarity	NPC207686
0.7937	Intermediate Similarity	NPC310118
0.7933	Intermediate Similarity	NPC138370
0.7928	Intermediate Similarity	NPC208084
0.7928	Intermediate Similarity	NPC74360
0.7919	Intermediate Similarity	NPC312645
0.7919	Intermediate Similarity	NPC169402
0.7917	Intermediate Similarity	NPC321428
0.7915	Intermediate Similarity	NPC141454
0.7911	Intermediate Similarity	NPC21638
0.7902	Intermediate Similarity	NPC284678
0.7883	Intermediate Similarity	NPC303658
0.788	Intermediate Similarity	NPC39679
0.787	Intermediate Similarity	NPC97902
0.7864	Intermediate Similarity	NPC39500
0.786	Intermediate Similarity	NPC49547
0.7848	Intermediate Similarity	NPC288987
0.7841	Intermediate Similarity	NPC74575
0.7818	Intermediate Similarity	NPC310211
0.7818	Intermediate Similarity	NPC308137
0.7816	Intermediate Similarity	NPC84478
0.7812	Intermediate Similarity	NPC174760
0.7807	Intermediate Similarity	NPC314954
0.7805	Intermediate Similarity	NPC191415
0.7804	Intermediate Similarity	NPC121772
0.7802	Intermediate Similarity	NPC240384
0.7802	Intermediate Similarity	NPC472061
0.7798	Intermediate Similarity	NPC82548
0.7797	Intermediate Similarity	NPC319232
0.7797	Intermediate Similarity	NPC24370
0.7788	Intermediate Similarity	NPC300156
0.7783	Intermediate Similarity	NPC279189
0.7783	Intermediate Similarity	NPC469554
0.7783	Intermediate Similarity	NPC13880
0.7783	Intermediate Similarity	NPC200553
0.7773	Intermediate Similarity	NPC146418
0.7773	Intermediate Similarity	NPC26543
0.7763	Intermediate Similarity	NPC157931
0.7763	Intermediate Similarity	NPC110151
0.7752	Intermediate Similarity	NPC244741
0.7743	Intermediate Similarity	NPC144452
0.7731	Intermediate Similarity	NPC295898
0.7723	Intermediate Similarity	NPC184408
0.7713	Intermediate Similarity	NPC322064
0.7713	Intermediate Similarity	NPC170114
0.771	Intermediate Similarity	NPC306376
0.7706	Intermediate Similarity	NPC101543
0.7695	Intermediate Similarity	NPC74619
0.7689	Intermediate Similarity	NPC198673
0.7689	Intermediate Similarity	NPC292958
0.7686	Intermediate Similarity	NPC478078
0.7682	Intermediate Similarity	NPC162002
0.7681	Intermediate Similarity	NPC102755
0.7675	Intermediate Similarity	NPC179287
0.7674	Intermediate Similarity	NPC81535
0.7672	Intermediate Similarity	NPC323752
0.7668	Intermediate Similarity	NPC470549
0.7667	Intermediate Similarity	NPC296527
0.7661	Intermediate Similarity	NPC472259
0.7661	Intermediate Similarity	NPC470500
0.7658	Intermediate Similarity	NPC264176
0.765	Intermediate Similarity	NPC184680
0.7647	Intermediate Similarity	NPC470020
0.7644	Intermediate Similarity	NPC96321
0.7644	Intermediate Similarity	NPC46561
0.7644	Intermediate Similarity	NPC247803
0.7644	Intermediate Similarity	NPC264285
0.7642	Intermediate Similarity	NPC470018
0.7639	Intermediate Similarity	NPC174489
0.7639	Intermediate Similarity	NPC315957
0.7634	Intermediate Similarity	NPC3207
0.7632	Intermediate Similarity	NPC322482
0.763	Intermediate Similarity	NPC76748
0.7617	Intermediate Similarity	NPC470785
0.7617	Intermediate Similarity	NPC79356
0.7617	Intermediate Similarity	NPC102592
0.7615	Intermediate Similarity	NPC53144
0.7615	Intermediate Similarity	NPC476098
0.7613	Intermediate Similarity	NPC82370
0.7613	Intermediate Similarity	NPC187501
0.7609	Intermediate Similarity	NPC192712
0.7609	Intermediate Similarity	NPC257851
0.7606	Intermediate Similarity	NPC307963
0.7605	Intermediate Similarity	NPC208522
0.7597	Intermediate Similarity	NPC473105
0.7594	Intermediate Similarity	NPC92111
0.7593	Intermediate Similarity	NPC476167
0.7591	Intermediate Similarity	NPC193238
0.7588	Intermediate Similarity	NPC216612
0.7586	Intermediate Similarity	NPC267853
0.7586	Intermediate Similarity	NPC474688
0.7583	Intermediate Similarity	NPC270515
0.7582	Intermediate Similarity	NPC63109
0.7577	Intermediate Similarity	NPC472099
0.7577	Intermediate Similarity	NPC150239
0.7576	Intermediate Similarity	NPC274640
0.7574	Intermediate Similarity	NPC26641
0.7572	Intermediate Similarity	NPC303374
0.7568	Intermediate Similarity	NPC5145
0.7558	Intermediate Similarity	NPC315491
0.7558	Intermediate Similarity	NPC45459
0.7558	Intermediate Similarity	NPC329747
0.7556	Intermediate Similarity	NPC330009
0.7554	Intermediate Similarity	NPC244897
0.7551	Intermediate Similarity	NPC216369
0.7546	Intermediate Similarity	NPC474916
0.7546	Intermediate Similarity	NPC239954
0.7546	Intermediate Similarity	NPC168911
0.7546	Intermediate Similarity	NPC192315
0.7545	Intermediate Similarity	NPC236668
0.7545	Intermediate Similarity	NPC221100
0.7545	Intermediate Similarity	NPC45190
0.7545	Intermediate Similarity	NPC469592
0.7545	Intermediate Similarity	NPC234078
0.7545	Intermediate Similarity	NPC471080
0.7544	Intermediate Similarity	NPC198503
0.7542	Intermediate Similarity	NPC470784
0.7536	Intermediate Similarity	NPC46580
0.7535	Intermediate Similarity	NPC251090
0.7534	Intermediate Similarity	NPC223427
0.7532	Intermediate Similarity	NPC473187
0.7532	Intermediate Similarity	NPC477549
0.7531	Intermediate Similarity	NPC78609
0.7524	Intermediate Similarity	NPC282103
0.7521	Intermediate Similarity	NPC141053
0.7511	Intermediate Similarity	NPC16352
0.7511	Intermediate Similarity	NPC146976
0.7511	Intermediate Similarity	NPC270918
0.7511	Intermediate Similarity	NPC315062
0.7511	Intermediate Similarity	NPC37152
0.75	Intermediate Similarity	NPC219087
0.75	Intermediate Similarity	NPC316981
0.75	Intermediate Similarity	NPC225279
0.7489	Intermediate Similarity	NPC39370
0.7489	Intermediate Similarity	NPC11464
0.7489	Intermediate Similarity	NPC471304
0.7489	Intermediate Similarity	NPC316411
0.7488	Intermediate Similarity	NPC62749
0.7479	Intermediate Similarity	NPC473186
0.7477	Intermediate Similarity	NPC171787

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 NPC260434 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	314
0.1-0.2	663
0.2-0.3	849
0.3-0.4	1530
0.4-0.5	2639
0.5-0.6	1935
0.6-0.7	1073
0.7-0.8	143
0.8-0.85	1
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9213	High Similarity	NPD2921	Clinical (unspecified phase)
0.8884	High Similarity	NPD5482	Discontinued
0.8789	High Similarity	NPD5483	Clinical (unspecified phase)
0.8432	Intermediate Similarity	NPD5450	Discontinued
0.8045	Intermediate Similarity	NPD5632	Approved
0.8035	Intermediate Similarity	NPD4958	Clinical (unspecified phase)
0.8028	Intermediate Similarity	NPD2121	Clinical (unspecified phase)
0.7991	Intermediate Similarity	NPD3006	Discontinued
0.792	Intermediate Similarity	NPD3259	Approved
0.7909	Intermediate Similarity	NPD5417	Clinical (unspecified phase)
0.7892	Intermediate Similarity	NPD6242	Discontinued
0.7883	Intermediate Similarity	NPD4429	Discontinued
0.7854	Intermediate Similarity	NPD6790	Phase 1
0.7806	Intermediate Similarity	NPD4558	Phase 2
0.7798	Intermediate Similarity	NPD2510	Approved
0.7798	Intermediate Similarity	NPD2509	Approved
0.7733	Intermediate Similarity	NPD1996	Discontinued
0.7713	Intermediate Similarity	NPD3394	Approved
0.7713	Intermediate Similarity	NPD3389	Approved
0.7713	Intermediate Similarity	NPD3393	Approved
0.7686	Intermediate Similarity	NPD7994	Phase 2
0.7661	Intermediate Similarity	NPD4795	Phase 2
0.7639	Intermediate Similarity	NPD1739	Approved
0.7639	Intermediate Similarity	NPD1740	Approved
0.7636	Intermediate Similarity	NPD5658	Approved
0.7619	Intermediate Similarity	NPD4952	Phase 3
0.7606	Intermediate Similarity	NPD1304	Clinical (unspecified phase)
0.7606	Intermediate Similarity	NPD1038	Approved
0.7588	Intermediate Similarity	NPD6160	Clinical (unspecified phase)
0.7558	Intermediate Similarity	NPD484	Approved
0.7543	Intermediate Similarity	NPD5022	Discontinued
0.7543	Intermediate Similarity	NPD5801	Clinical (unspecified phase)
0.7534	Intermediate Similarity	NPD5475	Discontinued
0.7534	Intermediate Similarity	NPD5416	Discontinued
0.7532	Intermediate Similarity	NPD7853	Phase 2
0.7522	Intermediate Similarity	NPD7823	Clinical (unspecified phase)
0.7521	Intermediate Similarity	NPD4373	Phase 2
0.7511	Intermediate Similarity	NPD1392	Approved
0.75	Intermediate Similarity	NPD4368	Phase 2
0.7479	Intermediate Similarity	NPD6525	Clinical (unspecified phase)
0.7469	Intermediate Similarity	NPD8049	Phase 2
0.7468	Intermediate Similarity	NPD5479	Discontinued
0.7466	Intermediate Similarity	NPD4862	Clinical (unspecified phase)
0.7459	Intermediate Similarity	NPD4926	Clinical (unspecified phase)
0.7449	Intermediate Similarity	NPD6228	Discontinued
0.7447	Intermediate Similarity	NPD7558	Phase 2
0.7412	Intermediate Similarity	NPD8405	Clinical (unspecified phase)
0.7404	Intermediate Similarity	NPD4885	Approved
0.7385	Intermediate Similarity	NPD4987	Clinical (unspecified phase)
0.7378	Intermediate Similarity	NPD6567	Clinical (unspecified phase)
0.7373	Intermediate Similarity	NPD5512	Phase 3
0.7373	Intermediate Similarity	NPD6741	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD8091	Phase 3
0.7359	Intermediate Similarity	NPD6824	Clinical (unspecified phase)
0.735	Intermediate Similarity	NPD5559	Phase 2
0.7342	Intermediate Similarity	NPD2951	Discontinued
0.7339	Intermediate Similarity	NPD7426	Phase 1
0.7339	Intermediate Similarity	NPD7603	Discontinued
0.7328	Intermediate Similarity	NPD7547	Clinical (unspecified phase)
0.7325	Intermediate Similarity	NPD5612	Discontinued
0.7325	Intermediate Similarity	NPD2412	Clinical (unspecified phase)
0.7317	Intermediate Similarity	NPD2311	Clinical (unspecified phase)
0.7309	Intermediate Similarity	NPD3003	Approved
0.7308	Intermediate Similarity	NPD7268	Clinical (unspecified phase)
0.7301	Intermediate Similarity	NPD7470	Discontinued
0.73	Intermediate Similarity	NPD5040	Clinical (unspecified phase)
0.7281	Intermediate Similarity	NPD5293	Phase 2
0.7273	Intermediate Similarity	NPD7393	Clinical (unspecified phase)
0.7269	Intermediate Similarity	NPD7069	Discontinued
0.7265	Intermediate Similarity	NPD3947	Discontinued
0.7265	Intermediate Similarity	NPD5901	Discontinued
0.7262	Intermediate Similarity	NPD7803	Approved
0.7229	Intermediate Similarity	NPD7404	Approved
0.7229	Intermediate Similarity	NPD6770	Approved
0.7225	Intermediate Similarity	NPD5067	Phase 2
0.7225	Intermediate Similarity	NPD5066	Phase 2
0.7215	Intermediate Similarity	NPD6962	Phase 2
0.7205	Intermediate Similarity	NPD6140	Clinical (unspecified phase)
0.7202	Intermediate Similarity	NPD802	Phase 2
0.72	Intermediate Similarity	NPD7956	Approved
0.72	Intermediate Similarity	NPD7955	Approved
0.7196	Intermediate Similarity	NPD4889	Approved
0.7195	Intermediate Similarity	NPD1768	Approved
0.7195	Intermediate Similarity	NPD3825	Phase 3
0.719	Intermediate Similarity	NPD749	Clinical (unspecified phase)
0.7186	Intermediate Similarity	NPD7395	Discontinued
0.7186	Intermediate Similarity	NPD3354	Phase 2
0.7182	Intermediate Similarity	NPD5003	Discontinued
0.7175	Intermediate Similarity	NPD7690	Clinical (unspecified phase)
0.7173	Intermediate Similarity	NPD1659	Phase 1
0.7171	Intermediate Similarity	NPD6531	Approved
0.7171	Intermediate Similarity	NPD6530	Approved
0.7169	Intermediate Similarity	NPD4418	Discontinued
0.716	Intermediate Similarity	NPD5018	Phase 3
0.7143	Intermediate Similarity	NPD3326	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD482	Approved
0.7143	Intermediate Similarity	NPD8100	Phase 3
0.7136	Intermediate Similarity	NPD3178	Discontinued
0.713	Intermediate Similarity	NPD5903	Approved
0.713	Intermediate Similarity	NPD5902	Approved
0.7121	Intermediate Similarity	NPD7689	Approved
0.7119	Intermediate Similarity	NPD3263	Phase 3
0.7118	Intermediate Similarity	NPD5866	Approved
0.7117	Intermediate Similarity	NPD4548	Discontinued
0.7117	Intermediate Similarity	NPD4118	Clinical (unspecified phase)
0.7112	Intermediate Similarity	NPD6568	Discontinued
0.7104	Intermediate Similarity	NPD7948	Phase 1
0.7103	Intermediate Similarity	NPD7708	Approved
0.7101	Intermediate Similarity	NPD8052	Clinical (unspecified phase)
0.71	Intermediate Similarity	NPD2433	Clinical (unspecified phase)
0.7098	Intermediate Similarity	NPD4442	Phase 2
0.7095	Intermediate Similarity	NPD5891	Approved
0.7093	Intermediate Similarity	NPD2189	Approved
0.7093	Intermediate Similarity	NPD2187	Approved
0.7091	Intermediate Similarity	NPD3324	Clinical (unspecified phase)
0.7091	Intermediate Similarity	NPD6861	Clinical (unspecified phase)
0.7087	Intermediate Similarity	NPD3945	Discontinued
0.7087	Intermediate Similarity	NPD3794	Approved
0.7087	Intermediate Similarity	NPD3795	Approved
0.7083	Intermediate Similarity	NPD4850	Phase 1
0.7082	Intermediate Similarity	NPD7194	Discontinued
0.7078	Intermediate Similarity	NPD1927	Discontinued
0.7078	Intermediate Similarity	NPD4372	Phase 1
0.7078	Intermediate Similarity	NPD6569	Phase 2
0.7076	Intermediate Similarity	NPD8279	Clinical (unspecified phase)
0.7073	Intermediate Similarity	NPD5488	Discontinued
0.7067	Intermediate Similarity	NPD6176	Phase 1
0.7066	Intermediate Similarity	NPD946	Discontinued
0.7061	Intermediate Similarity	NPD7067	Approved
0.7061	Intermediate Similarity	NPD4440	Clinical (unspecified phase)
0.7061	Intermediate Similarity	NPD7068	Approved
0.7061	Intermediate Similarity	NPD4506	Discontinued
0.7056	Intermediate Similarity	NPD7538	Clinical (unspecified phase)
0.7056	Intermediate Similarity	NPD8101	Phase 3
0.7054	Intermediate Similarity	NPD6964	Approved
0.7054	Intermediate Similarity	NPD6963	Approved
0.7052	Intermediate Similarity	NPD6961	Discontinued
0.7051	Intermediate Similarity	NPD7180	Phase 3
0.7049	Intermediate Similarity	NPD7417	Discontinued
0.7048	Intermediate Similarity	NPD5429	Discontinued
0.7045	Intermediate Similarity	NPD8358	Approved
0.7045	Intermediate Similarity	NPD3328	Phase 2
0.7043	Intermediate Similarity	NPD8363	Approved
0.7043	Intermediate Similarity	NPD8364	Approved
0.7042	Intermediate Similarity	NPD6263	Clinical (unspecified phase)
0.7036	Intermediate Similarity	NPD5116	Phase 1
0.7035	Intermediate Similarity	NPD3946	Clinical (unspecified phase)
0.7029	Intermediate Similarity	NPD8512	Phase 3
0.7023	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.702	Intermediate Similarity	NPD6716	Phase 1
0.7012	Intermediate Similarity	NPD8246	Approved
0.7012	Intermediate Similarity	NPD8247	Approved
0.7011	Intermediate Similarity	NPD7198	Clinical (unspecified phase)
0.7009	Intermediate Similarity	NPD4500	Approved
0.7009	Intermediate Similarity	NPD3402	Phase 1
0.7009	Intermediate Similarity	NPD4501	Approved
0.7004	Intermediate Similarity	NPD6247	Clinical (unspecified phase)
0.7004	Intermediate Similarity	NPD7925	Phase 2
0.7004	Intermediate Similarity	NPD5601	Phase 2
0.7004	Intermediate Similarity	NPD7924	Phase 2
0.7	Intermediate Similarity	NPD3924	Approved
0.7	Intermediate Similarity	NPD1867	Approved
0.7	Intermediate Similarity	NPD3923	Approved
0.7	Intermediate Similarity	NPD3921	Approved
0.7	Intermediate Similarity	NPD3922	Approved
0.6992	Remote Similarity	NPD8284	Discontinued
0.6992	Remote Similarity	NPD2285	Clinical (unspecified phase)
0.6988	Remote Similarity	NPD8365	Clinical (unspecified phase)
0.6988	Remote Similarity	NPD5509	Phase 1
0.6986	Remote Similarity	NPD2564	Approved
0.6986	Remote Similarity	NPD2565	Phase 2
0.6983	Remote Similarity	NPD3257	Approved
0.6982	Remote Similarity	NPD6550	Discontinued
0.6979	Remote Similarity	NPD5850	Phase 3
0.6974	Remote Similarity	NPD7222	Phase 2
0.6972	Remote Similarity	NPD8463	Approved
0.6972	Remote Similarity	NPD4948	Discontinued
0.697	Remote Similarity	NPD3815	Phase 1
0.697	Remote Similarity	NPD3816	Phase 1
0.6964	Remote Similarity	NPD2778	Approved
0.6955	Remote Similarity	NPD4454	Phase 2
0.6951	Remote Similarity	NPD6473	Phase 1
0.6949	Remote Similarity	NPD4923	Phase 1
0.6948	Remote Similarity	NPD6172	Clinical (unspecified phase)
0.6946	Remote Similarity	NPD4845	Discontinued
0.6944	Remote Similarity	NPD2095	Phase 2
0.6944	Remote Similarity	NPD2092	Phase 2
0.6944	Remote Similarity	NPD2094	Phase 2
0.6943	Remote Similarity	NPD7467	Discontinued
0.6942	Remote Similarity	NPD2472	Approved
0.6942	Remote Similarity	NPD6494	Phase 2
0.6942	Remote Similarity	NPD2471	Approved
0.694	Remote Similarity	NPD1322	Clinical (unspecified phase)
0.694	Remote Similarity	NPD3243	Approved
0.6939	Remote Similarity	NPD7886	Phase 2
0.6939	Remote Similarity	NPD7885	Phase 2
0.6934	Remote Similarity	NPD750	Phase 2
0.6933	Remote Similarity	NPD4396	Clinical (unspecified phase)
0.6929	Remote Similarity	NPD7284	Clinical (unspecified phase)
0.6929	Remote Similarity	NPD3801	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