NPASS Compound

Structure

CID89508 OpenBabel06191715422D 21 23 0 0 1 0 0 0 0 0999 V2000 -2.5079 1.6299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0363 0.9685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0361 -0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1973 1.4532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1969 -0.4854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8394 1.4539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2689 -2.2373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3576 0.9689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6789 0.9692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3574 -0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 0.9695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8387 -1.4536 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6787 -0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8390 -0.4847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8389 1.4542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5182 -0.4850 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.6947 -2.1357 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8023 -1.5552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7374 2.4178 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7241 1.0602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 8 2 0 0 0 0 5 10 2 0 0 0 0 6 9 2 0 0 0 0 6 11 1 0 0 0 0 7 12 1 0 0 0 0 7 18 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 9 13 1 0 0 0 0 10 16 1 0 0 0 0 11 15 1 0 0 0 0 11 17 2 0 0 0 0 12 14 1 0 0 0 0 12 19 1 1 0 0 0 13 14 2 0 0 0 0 13 16 1 0 0 0 0 14 17 1 0 0 0 0 15 20 2 0 0 0 0 15 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	286.1
Volume:	281.026
LogP:	1.516
LogD:	1.204
LogS:	-3.505
# Rotatable Bonds:	4
TPSA:	95.44
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.635
Synthetic Accessibility Score:	2.997
Fsp3:	0.2
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:	-5.027
MDCK Permeability:	6.017024134052917e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.157
20% Bioavailability (F20%):	0.046
30% Bioavailability (F30%):	0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.916
Plasma Protein Binding (PPB):	85.47638702392578%
Volume Distribution (VD):	0.605
Pgp-substrate:	13.945995330810547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.976
CYP1A2-substrate:	0.87
CYP2C19-inhibitor:	0.134
CYP2C19-substrate:	0.196
CYP2C9-inhibitor:	0.122
CYP2C9-substrate:	0.537
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.407
CYP3A4-inhibitor:	0.115
CYP3A4-substrate:	0.24

ADMET: Excretion

Clearance (CL):	6.786
Half-life (T1/2):	0.732

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.39
Drug-inuced Liver Injury (DILI):	0.968
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.094
Maximum Recommended Daily Dose:	0.866
Skin Sensitization:	0.088
Carcinogencity:	0.028
Eye Corrosion:	0.003
Eye Irritation:	0.102
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC89508

Natural Product ID:	NPC89508
*Common Name:**	Dichotomine C
IUPAC Name:	methyl 1-[(1R)-1,2-dihydroxyethyl]-9H-pyrido[3,4-b]indole-3-carboxylate
Synonyms:	Dichotomine C
Standard InCHIKey:	WKUVQUIYZHZZFT-LBPRGKRZSA-N
Standard InCHI:	InChI=1S/C15H14N2O4/c1-21-15(20)11-6-9-8-4-2-3-5-10(8)16-13(9)14(17-11)12(19)7-18/h2-6,12,16,18-19H,7H2,1H3/t12-/m0/s1
SMILES:	COC(=O)c1cc2c3ccccc3[nH]c2c([C@H](CO)O)n1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL458036
PubChem CID:	11254673
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
NPO11597	Stellaria dichotoma	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387643]
NPO11597.1	Stellaria dichotoma var. lanceolata	Under-species	Caryophyllaceae	Eukaryota	n.a.	root	n.a.	PMID[15467234]
NPO11597	Stellaria dichotoma	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16309326]
NPO11597.1	Stellaria dichotoma var. lanceolata	Under-species	Caryophyllaceae	Eukaryota	n.a.	root	n.a.	PMID[21090796]
NPO11597.1	Stellaria dichotoma var. lanceolata	Under-species	Caryophyllaceae	Eukaryota	roots	n.a.	n.a.	PMID[21090796]
NPO11597.1	Stellaria dichotoma var. lanceolata	Under-species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11597.1	Stellaria dichotoma var. lanceolata	Under-species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11597	Stellaria dichotoma	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11597	Stellaria dichotoma	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11597	Stellaria dichotoma	Species	Caryophyllaceae	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	3
Others	1

Activity Type	# Activity
Cell Line	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	Inhibition	=	89.2	%	PMID[454227]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	IC50	=	62000.0	nM	PMID[454227]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	IC50	=	19000.0	nM	PMID[454227]
NPT521	Cell Line	RBL-2H3	Rattus norvegicus	IC50	=	15000.0	nM	PMID[454227]

☑ 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 NPC89508 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	296
0.1-0.2	1631
0.2-0.3	8225
0.3-0.4	12679
0.4-0.5	14575
0.5-0.6	2589
0.6-0.7	2176
0.7-0.8	491
0.8-0.85	25
0.85-0.9	4
0.9-0.95	3
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.9844	High Similarity	NPC312645
0.9683	High Similarity	NPC244741
0.9524	High Similarity	NPC165599
0.9206	High Similarity	NPC141454
0.9171	High Similarity	NPC132539
0.8856	High Similarity	NPC477979
0.885	High Similarity	NPC118940
0.8726	High Similarity	NPC57453
0.8519	High Similarity	NPC314394
0.8473	Intermediate Similarity	NPC123839
0.8465	Intermediate Similarity	NPC266249
0.8378	Intermediate Similarity	NPC165964
0.8341	Intermediate Similarity	NPC473800
0.8308	Intermediate Similarity	NPC57398
0.8247	Intermediate Similarity	NPC160381
0.8235	Intermediate Similarity	NPC321428
0.8169	Intermediate Similarity	NPC229893
0.8146	Intermediate Similarity	NPC315545
0.8146	Intermediate Similarity	NPC314297
0.8143	Intermediate Similarity	NPC472285
0.8098	Intermediate Similarity	NPC313345
0.8098	Intermediate Similarity	NPC315638
0.8098	Intermediate Similarity	NPC314855
0.8098	Intermediate Similarity	NPC313796
0.8082	Intermediate Similarity	NPC182222
0.8049	Intermediate Similarity	NPC314648
0.8029	Intermediate Similarity	NPC314834
0.8028	Intermediate Similarity	NPC260434
0.8019	Intermediate Similarity	NPC39679
0.8009	Intermediate Similarity	NPC36405
0.7962	Intermediate Similarity	NPC118228
0.7938	Intermediate Similarity	NPC219336
0.7934	Intermediate Similarity	NPC184408
0.7921	Intermediate Similarity	NPC79356
0.7921	Intermediate Similarity	NPC102592
0.7913	Intermediate Similarity	NPC476098
0.7905	Intermediate Similarity	NPC82370
0.7905	Intermediate Similarity	NPC87413
0.7897	Intermediate Similarity	NPC469896
0.7887	Intermediate Similarity	NPC217372
0.7887	Intermediate Similarity	NPC183662
0.7887	Intermediate Similarity	NPC15573
0.7848	Intermediate Similarity	NPC15801
0.7845	Intermediate Similarity	NPC258048
0.7824	Intermediate Similarity	NPC60621
0.7816	Intermediate Similarity	NPC471944
0.781	Intermediate Similarity	NPC325297
0.78	Intermediate Similarity	NPC221873
0.7799	Intermediate Similarity	NPC270918
0.7778	Intermediate Similarity	NPC322644
0.7757	Intermediate Similarity	NPC3207
0.7752	Intermediate Similarity	NPC475271
0.7751	Intermediate Similarity	NPC300156
0.7746	Intermediate Similarity	NPC39500
0.7744	Intermediate Similarity	NPC151635
0.7744	Intermediate Similarity	NPC84347
0.7714	Intermediate Similarity	NPC4687
0.7703	Intermediate Similarity	NPC474701
0.77	Intermediate Similarity	NPC62749
0.7696	Intermediate Similarity	NPC174760
0.7692	Intermediate Similarity	NPC33949
0.7688	Intermediate Similarity	NPC284678
0.7688	Intermediate Similarity	NPC207851
0.7671	Intermediate Similarity	NPC122436
0.7671	Intermediate Similarity	NPC51388
0.7665	Intermediate Similarity	NPC475844
0.7664	Intermediate Similarity	NPC472291
0.7647	Intermediate Similarity	NPC472295
0.7647	Intermediate Similarity	NPC472210
0.7647	Intermediate Similarity	NPC247735
0.7647	Intermediate Similarity	NPC230403
0.7647	Intermediate Similarity	NPC81802
0.7647	Intermediate Similarity	NPC269886
0.7638	Intermediate Similarity	NPC48938
0.7624	Intermediate Similarity	NPC102338
0.7624	Intermediate Similarity	NPC63199
0.7624	Intermediate Similarity	NPC196251
0.7624	Intermediate Similarity	NPC111602
0.7613	Intermediate Similarity	NPC274640
0.7613	Intermediate Similarity	NPC194740
0.7612	Intermediate Similarity	NPC90415
0.7612	Intermediate Similarity	NPC194040
0.7596	Intermediate Similarity	NPC214428
0.7593	Intermediate Similarity	NPC152768
0.7593	Intermediate Similarity	NPC148183
0.7593	Intermediate Similarity	NPC322064
0.7588	Intermediate Similarity	NPC148889
0.7585	Intermediate Similarity	NPC306376
0.7583	Intermediate Similarity	NPC45190
0.7583	Intermediate Similarity	NPC472287
0.7583	Intermediate Similarity	NPC472286
0.7577	Intermediate Similarity	NPC470784
0.7576	Intermediate Similarity	NPC107836
0.757	Intermediate Similarity	NPC187501
0.757	Intermediate Similarity	NPC294375
0.7557	Intermediate Similarity	NPC179287
0.7549	Intermediate Similarity	NPC138370
0.7547	Intermediate Similarity	NPC283117
0.7547	Intermediate Similarity	NPC249583
0.7545	Intermediate Similarity	NPC267853
0.7537	Intermediate Similarity	NPC175474
0.7534	Intermediate Similarity	NPC323969
0.7533	Intermediate Similarity	NPC184680
0.7525	Intermediate Similarity	NPC315555
0.7524	Intermediate Similarity	NPC276517
0.7524	Intermediate Similarity	NPC220151
0.7524	Intermediate Similarity	NPC19692
0.7523	Intermediate Similarity	NPC247803
0.7523	Intermediate Similarity	NPC82070
0.7512	Intermediate Similarity	NPC312870
0.7512	Intermediate Similarity	NPC294909
0.7512	Intermediate Similarity	NPC254240
0.7512	Intermediate Similarity	NPC199851
0.7512	Intermediate Similarity	NPC128265
0.7512	Intermediate Similarity	NPC55493
0.7511	Intermediate Similarity	NPC244897
0.75	Intermediate Similarity	NPC277350
0.75	Intermediate Similarity	NPC470785
0.75	Intermediate Similarity	NPC221100
0.75	Intermediate Similarity	NPC317752
0.75	Intermediate Similarity	NPC31700
0.75	Intermediate Similarity	NPC83111
0.75	Intermediate Similarity	NPC234078
0.7489	Intermediate Similarity	NPC208084
0.7489	Intermediate Similarity	NPC288987
0.7489	Intermediate Similarity	NPC52254
0.7488	Intermediate Similarity	NPC245916
0.7487	Intermediate Similarity	NPC256268
0.7487	Intermediate Similarity	NPC470894
0.7477	Intermediate Similarity	NPC169402
0.7467	Intermediate Similarity	NPC474688
0.7466	Intermediate Similarity	NPC144452
0.7465	Intermediate Similarity	NPC116238
0.7464	Intermediate Similarity	NPC241024
0.7464	Intermediate Similarity	NPC123395
0.7463	Intermediate Similarity	NPC243058
0.7455	Intermediate Similarity	NPC150239
0.7454	Intermediate Similarity	NPC244856
0.7454	Intermediate Similarity	NPC318299
0.7445	Intermediate Similarity	NPC316411
0.7442	Intermediate Similarity	NPC234999
0.7442	Intermediate Similarity	NPC303951
0.7437	Intermediate Similarity	NPC219848
0.7431	Intermediate Similarity	NPC476114
0.743	Intermediate Similarity	NPC470280
0.743	Intermediate Similarity	NPC86834
0.743	Intermediate Similarity	NPC210828
0.7429	Intermediate Similarity	NPC79129
0.7429	Intermediate Similarity	NPC249150
0.7429	Intermediate Similarity	NPC49196
0.7429	Intermediate Similarity	NPC195461
0.7429	Intermediate Similarity	NPC81654
0.7429	Intermediate Similarity	NPC313985
0.7427	Intermediate Similarity	NPC67551
0.7426	Intermediate Similarity	NPC203635
0.7418	Intermediate Similarity	NPC317373
0.7416	Intermediate Similarity	NPC52557
0.7416	Intermediate Similarity	NPC474916
0.7411	Intermediate Similarity	NPC192712
0.7407	Intermediate Similarity	NPC9894
0.7407	Intermediate Similarity	NPC23294
0.7406	Intermediate Similarity	NPC223427
0.7404	Intermediate Similarity	NPC472293
0.7402	Intermediate Similarity	NPC278434
0.7399	Intermediate Similarity	NPC21638
0.7397	Intermediate Similarity	NPC27041
0.7393	Intermediate Similarity	NPC91868
0.7393	Intermediate Similarity	NPC63971
0.7386	Intermediate Similarity	NPC152620
0.7383	Intermediate Similarity	NPC88008
0.7381	Intermediate Similarity	NPC472297
0.7381	Intermediate Similarity	NPC280714
0.7381	Intermediate Similarity	NPC472296
0.738	Intermediate Similarity	NPC235685
0.7374	Intermediate Similarity	NPC252572
0.7373	Intermediate Similarity	NPC308137
0.7373	Intermediate Similarity	NPC310211
0.7371	Intermediate Similarity	NPC327592
0.7364	Intermediate Similarity	NPC74619
0.7364	Intermediate Similarity	NPC281049
0.7361	Intermediate Similarity	NPC5145
0.7358	Intermediate Similarity	NPC476874
0.7357	Intermediate Similarity	NPC207686
0.7356	Intermediate Similarity	NPC57994
0.7356	Intermediate Similarity	NPC289299
0.7352	Intermediate Similarity	NPC85702
0.7348	Intermediate Similarity	NPC101350
0.7347	Intermediate Similarity	NPC470509
0.7343	Intermediate Similarity	NPC472292
0.7339	Intermediate Similarity	NPC471080
0.7339	Intermediate Similarity	NPC236424
0.7339	Intermediate Similarity	NPC469592
0.7339	Intermediate Similarity	NPC306644
0.7333	Intermediate Similarity	NPC50503
0.7333	Intermediate Similarity	NPC472284
0.7333	Intermediate Similarity	NPC261251
0.7333	Intermediate Similarity	NPC67288
0.7331	Intermediate Similarity	NPC14812
0.733	Intermediate Similarity	NPC74360
0.733	Intermediate Similarity	NPC324091

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 NPC89508 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	206
0.1-0.2	549
0.2-0.3	732
0.3-0.4	1551
0.4-0.5	2917
0.5-0.6	2261
0.6-0.7	812
0.7-0.8	119
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8182	Intermediate Similarity	NPD2921	Clinical (unspecified phase)
0.815	Intermediate Similarity	NPD5003	Discontinued
0.8036	Intermediate Similarity	NPD5483	Clinical (unspecified phase)
0.794	Intermediate Similarity	NPD2565	Phase 2
0.794	Intermediate Similarity	NPD2564	Approved
0.7895	Intermediate Similarity	NPD4506	Discontinued
0.7895	Intermediate Similarity	NPD5482	Discontinued
0.7751	Intermediate Similarity	NPD2715	Clinical (unspecified phase)
0.774	Intermediate Similarity	NPD2121	Clinical (unspecified phase)
0.7731	Intermediate Similarity	NPD6770	Approved
0.7706	Intermediate Similarity	NPD6160	Clinical (unspecified phase)
0.7703	Intermediate Similarity	NPD2721	Clinical (unspecified phase)
0.77	Intermediate Similarity	NPD6657	Clinical (unspecified phase)
0.7604	Intermediate Similarity	NPD5632	Approved
0.7594	Intermediate Similarity	NPD2510	Approved
0.7594	Intermediate Similarity	NPD2509	Approved
0.7589	Intermediate Similarity	NPD6263	Clinical (unspecified phase)
0.7585	Intermediate Similarity	NPD7946	Pre-registration
0.7577	Intermediate Similarity	NPD2844	Phase 3
0.7573	Intermediate Similarity	NPD5450	Discontinued
0.7571	Intermediate Similarity	NPD2920	Discontinued
0.7546	Intermediate Similarity	NPD5417	Clinical (unspecified phase)
0.7536	Intermediate Similarity	NPD5901	Discontinued
0.7523	Intermediate Similarity	NPD4900	Clinical (unspecified phase)
0.7512	Intermediate Similarity	NPD3389	Approved
0.7512	Intermediate Similarity	NPD4501	Approved
0.7512	Intermediate Similarity	NPD3394	Approved
0.7512	Intermediate Similarity	NPD3393	Approved
0.7512	Intermediate Similarity	NPD4500	Approved
0.75	Intermediate Similarity	NPD4987	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD4862	Clinical (unspecified phase)
0.7488	Intermediate Similarity	NPD7470	Discontinued
0.7488	Intermediate Similarity	NPD5416	Discontinued
0.7431	Intermediate Similarity	NPD8160	Phase 2
0.7429	Intermediate Similarity	NPD4601	Approved
0.7429	Intermediate Similarity	NPD4600	Approved
0.7418	Intermediate Similarity	NPD4901	Clinical (unspecified phase)
0.7376	Intermediate Similarity	NPD1996	Discontinued
0.7356	Intermediate Similarity	NPD4602	Approved
0.7347	Intermediate Similarity	NPD4554	Clinical (unspecified phase)
0.7339	Intermediate Similarity	NPD3795	Approved
0.7339	Intermediate Similarity	NPD3794	Approved
0.7327	Intermediate Similarity	NPD3178	Discontinued
0.7324	Intermediate Similarity	NPD6176	Phase 1
0.7317	Intermediate Similarity	NPD4948	Discontinued
0.7313	Intermediate Similarity	NPD7688	Phase 1
0.7289	Intermediate Similarity	NPD8289	Discontinued
0.725	Intermediate Similarity	NPD4736	Clinical (unspecified phase)
0.723	Intermediate Similarity	NPD7727	Phase 2
0.7228	Intermediate Similarity	NPD5398	Clinical (unspecified phase)
0.7217	Intermediate Similarity	NPD2951	Discontinued
0.7215	Intermediate Similarity	NPD8096	Phase 3
0.7215	Intermediate Similarity	NPD8097	Phase 3
0.7214	Intermediate Similarity	NPD749	Clinical (unspecified phase)
0.7212	Intermediate Similarity	NPD5912	Clinical (unspecified phase)
0.7212	Intermediate Similarity	NPD5913	Phase 3
0.7206	Intermediate Similarity	NPD5596	Phase 2
0.7203	Intermediate Similarity	NPD3328	Phase 2
0.7195	Intermediate Similarity	NPD2433	Clinical (unspecified phase)
0.7193	Intermediate Similarity	NPD5479	Discontinued
0.7189	Intermediate Similarity	NPD8399	Phase 1
0.7189	Intermediate Similarity	NPD8423	Phase 2
0.7183	Intermediate Similarity	NPD484	Approved
0.7182	Intermediate Similarity	NPD3243	Approved
0.7179	Intermediate Similarity	NPD6716	Phase 1
0.7176	Intermediate Similarity	NPD6732	Clinical (unspecified phase)
0.7176	Intermediate Similarity	NPD7001	Phase 3
0.7169	Intermediate Similarity	NPD5475	Discontinued
0.7164	Intermediate Similarity	NPD482	Approved
0.7163	Intermediate Similarity	NPD4499	Approved
0.7156	Intermediate Similarity	NPD5512	Phase 3
0.7156	Intermediate Similarity	NPD6995	Phase 1
0.7149	Intermediate Similarity	NPD3757	Clinical (unspecified phase)
0.713	Intermediate Similarity	NPD56	Approved
0.713	Intermediate Similarity	NPD8283	Approved
0.713	Intermediate Similarity	NPD8115	Approved
0.713	Intermediate Similarity	NPD8114	Approved
0.713	Intermediate Similarity	NPD3947	Discontinued
0.713	Intermediate Similarity	NPD8098	Approved
0.713	Intermediate Similarity	NPD8282	Approved
0.7125	Intermediate Similarity	NPD8463	Approved
0.7122	Intermediate Similarity	NPD2092	Phase 2
0.7122	Intermediate Similarity	NPD2095	Phase 2
0.7122	Intermediate Similarity	NPD2094	Phase 2
0.7115	Intermediate Similarity	NPD1534	Approved
0.7105	Intermediate Similarity	NPD7268	Clinical (unspecified phase)
0.7105	Intermediate Similarity	NPD6292	Clinical (unspecified phase)
0.71	Intermediate Similarity	NPD4373	Phase 2
0.7098	Intermediate Similarity	NPD3258	Approved
0.7097	Intermediate Similarity	NPD3003	Approved
0.7094	Intermediate Similarity	NPD6641	Approved
0.7094	Intermediate Similarity	NPD6642	Approved
0.7087	Intermediate Similarity	NPD2096	Phase 2
0.7087	Intermediate Similarity	NPD2091	Phase 2
0.7087	Intermediate Similarity	NPD1096	Discontinued
0.708	Intermediate Similarity	NPD6824	Clinical (unspecified phase)
0.7071	Intermediate Similarity	NPD1631	Approved
0.707	Intermediate Similarity	NPD7817	Phase 1
0.7067	Intermediate Similarity	NPD6141	Clinical (unspecified phase)
0.7067	Intermediate Similarity	NPD3280	Approved
0.7059	Intermediate Similarity	NPD5866	Approved
0.7056	Intermediate Similarity	NPD6248	Phase 2
0.7056	Intermediate Similarity	NPD6249	Phase 2
0.7056	Intermediate Similarity	NPD3746	Discontinued
0.7056	Intermediate Similarity	NPD4885	Approved
0.7054	Intermediate Similarity	NPD7878	Phase 2
0.7054	Intermediate Similarity	NPD7395	Discontinued
0.7046	Intermediate Similarity	NPD7921	Approved
0.7045	Intermediate Similarity	NPD648	Clinical (unspecified phase)
0.7045	Intermediate Similarity	NPD7998	Clinical (unspecified phase)
0.7039	Intermediate Similarity	NPD7853	Phase 2
0.7039	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.7031	Intermediate Similarity	NPD4328	Approved
0.7029	Intermediate Similarity	NPD4558	Phase 2
0.7009	Intermediate Similarity	NPD53	Approved
0.7009	Intermediate Similarity	NPD4958	Clinical (unspecified phase)
0.7009	Intermediate Similarity	NPD7778	Approved
0.7009	Intermediate Similarity	NPD7777	Approved
0.6996	Remote Similarity	NPD5902	Approved
0.6996	Remote Similarity	NPD3257	Approved
0.6996	Remote Similarity	NPD7538	Clinical (unspecified phase)
0.6996	Remote Similarity	NPD5903	Approved
0.6996	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.699	Remote Similarity	NPD1783	Clinical (unspecified phase)
0.698	Remote Similarity	NPD7708	Approved
0.6977	Remote Similarity	NPD1768	Approved
0.6974	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.697	Remote Similarity	NPD4952	Phase 3
0.697	Remote Similarity	NPD5022	Discontinued
0.6967	Remote Similarity	NPD5592	Clinical (unspecified phase)
0.6966	Remote Similarity	NPD3006	Discontinued
0.6964	Remote Similarity	NPD6456	Discontinued
0.6959	Remote Similarity	NPD2779	Approved
0.6957	Remote Similarity	NPD3259	Approved
0.6955	Remote Similarity	NPD6376	Discontinued
0.6955	Remote Similarity	NPD7947	Clinical (unspecified phase)
0.6952	Remote Similarity	NPD4334	Discontinued
0.695	Remote Similarity	NPD2915	Discontinued
0.6946	Remote Similarity	NPD750	Phase 2
0.6946	Remote Similarity	NPD5488	Discontinued
0.6942	Remote Similarity	NPD6452	Discontinued
0.694	Remote Similarity	NPD6962	Phase 2
0.694	Remote Similarity	NPD1867	Approved
0.6936	Remote Similarity	NPD4368	Phase 2
0.6935	Remote Similarity	NPD7803	Approved
0.6931	Remote Similarity	NPD1325	Approved
0.6931	Remote Similarity	NPD1573	Approved
0.6931	Remote Similarity	NPD1326	Approved
0.6931	Remote Similarity	NPD1575	Approved
0.6927	Remote Similarity	NPD5487	Phase 1
0.6923	Remote Similarity	NPD4520	Approved
0.692	Remote Similarity	NPD4897	Phase 2
0.6919	Remote Similarity	NPD1630	Approved
0.6916	Remote Similarity	NPD6242	Discontinued
0.6913	Remote Similarity	NPD7603	Discontinued
0.6909	Remote Similarity	NPD6838	Clinical (unspecified phase)
0.6909	Remote Similarity	NPD8322	Phase 2
0.6898	Remote Similarity	NPD3800	Clinical (unspecified phase)
0.6887	Remote Similarity	NPD3785	Clinical (unspecified phase)
0.6883	Remote Similarity	NPD6978	Phase 2
0.6883	Remote Similarity	NPD7994	Phase 2
0.6883	Remote Similarity	NPD6977	Clinical (unspecified phase)
0.6881	Remote Similarity	NPD5721	Clinical (unspecified phase)
0.688	Remote Similarity	NPD5040	Clinical (unspecified phase)
0.6872	Remote Similarity	NPD7404	Approved
0.6872	Remote Similarity	NPD7194	Discontinued
0.687	Remote Similarity	NPD7955	Approved
0.687	Remote Similarity	NPD7956	Approved
0.687	Remote Similarity	NPD6247	Clinical (unspecified phase)
0.6854	Remote Similarity	NPD4376	Phase 3
0.6853	Remote Similarity	NPD1571	Phase 2
0.6853	Remote Similarity	NPD8364	Approved
0.6853	Remote Similarity	NPD8363	Approved
0.6852	Remote Similarity	NPD4397	Phase 1
0.6847	Remote Similarity	NPD7941	Phase 3
0.6842	Remote Similarity	NPD6530	Approved
0.6842	Remote Similarity	NPD6531	Approved
0.684	Remote Similarity	NPD3263	Phase 3
0.6836	Remote Similarity	NPD7181	Phase 3
0.6835	Remote Similarity	NPD5017	Discontinued
0.6833	Remote Similarity	NPD5429	Discontinued
0.6828	Remote Similarity	NPD4429	Discontinued
0.6828	Remote Similarity	NPD8405	Clinical (unspecified phase)
0.6824	Remote Similarity	NPD7589	Clinical (unspecified phase)
0.6822	Remote Similarity	NPD5891	Approved
0.682	Remote Similarity	NPD7000	Clinical (unspecified phase)
0.682	Remote Similarity	NPD2778	Approved
0.682	Remote Similarity	NPD6999	Discontinued
0.6818	Remote Similarity	NPD5426	Phase 3
0.6818	Remote Similarity	NPD7712	Clinical (unspecified phase)
0.6812	Remote Similarity	NPD1587	Approved
0.6809	Remote Similarity	NPD7558	Phase 2
0.6806	Remote Similarity	NPD6206	Phase 1
0.6802	Remote Similarity	NPD5658	Approved
0.68	Remote Similarity	NPD3945	Discontinued
0.6798	Remote Similarity	NPD8365	Clinical (unspecified phase)
0.6797	Remote Similarity	NPD6976	Clinical (unspecified phase)
0.6796	Remote Similarity	NPD2382	Approved
0.6796	Remote Similarity	NPD5104	Approved
0.6796	Remote Similarity	NPD2381	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