NPASS Compound

Structure

NPC280852 OpenBabel07101719522D 33 39 0 0 1 0 0 0 0 0999 V2000 -3.6720 3.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6720 2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5955 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9836 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1888 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5768 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0078 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3958 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1943 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5823 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2701 2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6581 2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4041 2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2079 2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6720 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9400 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9400 2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8060 2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8060 1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0132 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2701 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6581 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6065 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5380 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0739 1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4041 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2079 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5380 2.4781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.6120 -0.0000 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 -1.0739 2.4781 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 2 0 0 0 0 3 5 2 0 0 0 0 3 7 1 0 0 0 0 4 6 2 0 0 0 0 4 8 1 0 0 0 0 5 9 1 0 0 0 0 6 10 1 0 0 0 0 7 20 2 0 0 0 0 8 21 2 0 0 0 0 9 24 2 0 0 0 0 10 25 2 0 0 0 0 11 13 2 0 0 0 0 11 22 1 0 0 0 0 12 14 1 0 0 0 0 12 23 1 0 0 0 0 13 30 1 0 0 0 0 14 33 1 0 0 0 0 15 26 1 0 0 0 0 16 19 1 0 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 17 33 1 0 0 0 0 18 19 1 0 0 0 0 19 15 1 6 0 0 0 20 22 1 0 0 0 0 20 24 1 0 0 0 0 21 23 1 0 0 0 0 21 25 1 0 0 0 0 22 28 2 0 0 0 0 23 29 2 0 0 0 0 24 31 1 0 0 0 0 25 32 1 0 0 0 0 26 28 1 0 0 0 0 26 30 2 0 0 0 0 27 29 1 0 0 0 0 27 33 1 6 0 0 0 28 31 1 0 0 0 0 29 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.23
Volume:	465.231
LogP:	5.772
LogD:	4.636
LogS:	-5.114
# Rotatable Bonds:	2
TPSA:	47.71
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.321
Synthetic Accessibility Score:	3.716
Fsp3:	0.276
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.632
MDCK Permeability:	1.2613450053322595e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.942
30% Bioavailability (F30%):	0.646

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.588
Plasma Protein Binding (PPB):	98.21192169189453%
Volume Distribution (VD):	1.647
Pgp-substrate:	1.7000300884246826%

ADMET: Metabolism

CYP1A2-inhibitor:	0.936
CYP1A2-substrate:	0.951
CYP2C19-inhibitor:	0.91
CYP2C19-substrate:	0.132
CYP2C9-inhibitor:	0.583
CYP2C9-substrate:	0.768
CYP2D6-inhibitor:	0.924
CYP2D6-substrate:	0.908
CYP3A4-inhibitor:	0.72
CYP3A4-substrate:	0.827

ADMET: Excretion

Clearance (CL):	4.386
Half-life (T1/2):	0.096

ADMET: Toxicity

hERG Blockers:	0.821
Human Hepatotoxicity (H-HT):	0.752
Drug-inuced Liver Injury (DILI):	0.782
AMES Toxicity:	0.552
Rat Oral Acute Toxicity:	0.991
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.502
Carcinogencity:	0.399
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.988

Download Data

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

Natural Product: NPC280852

Natural Product ID:	NPC280852
*Common Name:**	Usambarensine
IUPAC Name:	(2R,3E,12bS)-3-ethylidene-2-(9H-pyrido[3,4-b]indol-1-ylmethyl)-2,4,6,7,12,12b-hexahydro-1H-indolo[2,3-a]quinolizine
Synonyms:	Usambarensine
Standard InCHIKey:	VUMZOPMHFVDIMF-NLLHOBBWSA-N
Standard InCHI:	InChI=1S/C29H28N4/c1-2-18-17-33-14-12-23-21-8-4-6-10-25(21)32-29(23)27(33)16-19(18)15-26-28-22(11-13-30-26)20-7-3-5-9-24(20)31-28/h2-11,13,19,27,31-32H,12,14-17H2,1H3/b18-2-/t19-,27-/m0/s1
SMILES:	C/C=C1/CN2CCc3c4ccccc4[nH]c3[C@@H]2C[C@@H]1Cc1c2c(ccn1)c1ccccc1[nH]2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL490322
PubChem CID:	5281413
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
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	roots	n.a.	n.a.	PMID[10217724]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12398531]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	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
Others	6

Activity Type	# Activity
Cell Line	1
Organism	8
Others	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	9700.0	nM	PMID[570507]
NPT27	Others	Unspecified		IC50	=	4620.0	nM	PMID[570507]
NPT2	Others	Unspecified		Ratio IC50	=	14.8	n.a.	PMID[570507]
NPT2	Others	Unspecified		Ratio IC50	=	36.6	n.a.	PMID[570507]
NPT2	Others	Unspecified		Ratio IC50	=	3.1	n.a.	PMID[570507]
NPT2	Others	Unspecified		Ratio IC50	=	7.8	n.a.	PMID[570507]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1520.0	nM	PMID[570508]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	594.0	nM	PMID[570508]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	4410.0	nM	PMID[570508]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	4830.0	nM	PMID[570508]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.655	ug.mL-1	PMID[570509]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.265	ug.mL-1	PMID[570509]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	2000.0	nM	PMID[570510]
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	0.49	ug.mL-1	PMID[570511]

☑ 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 NPC280852 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	996
0.1-0.2	10443
0.2-0.3	21312
0.3-0.4	4696
0.4-0.5	1981
0.5-0.6	1701
0.6-0.7	1103
0.7-0.8	391
0.8-0.85	56
0.85-0.9	14
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9241	High Similarity	NPC229173
0.9057	High Similarity	NPC221786
0.9057	High Similarity	NPC474880
0.9006	High Similarity	NPC317105
0.8924	High Similarity	NPC325903
0.8902	High Similarity	NPC474897
0.882	High Similarity	NPC475990
0.8797	High Similarity	NPC53947
0.879	High Similarity	NPC201380
0.879	High Similarity	NPC179787
0.8786	High Similarity	NPC231536
0.8734	High Similarity	NPC321911
0.8726	High Similarity	NPC63545
0.8671	High Similarity	NPC469811
0.8642	High Similarity	NPC216643
0.8625	High Similarity	NPC470233
0.8608	High Similarity	NPC288838
0.8485	Intermediate Similarity	NPC470203
0.8424	Intermediate Similarity	NPC122141
0.8424	Intermediate Similarity	NPC470204
0.8415	Intermediate Similarity	NPC236711
0.8364	Intermediate Similarity	NPC56765
0.8344	Intermediate Similarity	NPC88097
0.8333	Intermediate Similarity	NPC40070
0.8256	Intermediate Similarity	NPC474958
0.8253	Intermediate Similarity	NPC135141
0.8253	Intermediate Similarity	NPC92796
0.8228	Intermediate Similarity	NPC73767
0.821	Intermediate Similarity	NPC470111
0.8204	Intermediate Similarity	NPC44773
0.8204	Intermediate Similarity	NPC215584
0.8198	Intermediate Similarity	NPC471579
0.8187	Intermediate Similarity	NPC82331
0.8182	Intermediate Similarity	NPC476219
0.8177	Intermediate Similarity	NPC476041
0.8177	Intermediate Similarity	NPC304926
0.8176	Intermediate Similarity	NPC469761
0.8176	Intermediate Similarity	NPC469783
0.8176	Intermediate Similarity	NPC115611
0.8176	Intermediate Similarity	NPC469767
0.8176	Intermediate Similarity	NPC469784
0.8176	Intermediate Similarity	NPC469779
0.8176	Intermediate Similarity	NPC469768
0.8176	Intermediate Similarity	NPC469780
0.8144	Intermediate Similarity	NPC318065
0.8144	Intermediate Similarity	NPC206819
0.8125	Intermediate Similarity	NPC469766
0.8113	Intermediate Similarity	NPC110126
0.8101	Intermediate Similarity	NPC84911
0.8098	Intermediate Similarity	NPC21605
0.8089	Intermediate Similarity	NPC198988
0.8063	Intermediate Similarity	NPC284635
0.8059	Intermediate Similarity	NPC274229
0.8038	Intermediate Similarity	NPC96102
0.8038	Intermediate Similarity	NPC325252
0.8038	Intermediate Similarity	NPC261195
0.8038	Intermediate Similarity	NPC29886
0.8036	Intermediate Similarity	NPC41257
0.8035	Intermediate Similarity	NPC477611
0.8023	Intermediate Similarity	NPC97343
0.8012	Intermediate Similarity	NPC63157
0.8012	Intermediate Similarity	NPC473868
0.8	Intermediate Similarity	NPC59269
0.7989	Intermediate Similarity	NPC297034
0.7987	Intermediate Similarity	NPC251722
0.7987	Intermediate Similarity	NPC314102
0.7987	Intermediate Similarity	NPC105127
0.7976	Intermediate Similarity	NPC286427
0.7963	Intermediate Similarity	NPC20144
0.795	Intermediate Similarity	NPC59084
0.7946	Intermediate Similarity	NPC265576
0.7941	Intermediate Similarity	NPC225018
0.7933	Intermediate Similarity	NPC99939
0.7933	Intermediate Similarity	NPC308931
0.7933	Intermediate Similarity	NPC15102
0.7923	Intermediate Similarity	NPC326422
0.7895	Intermediate Similarity	NPC473362
0.7895	Intermediate Similarity	NPC166492
0.7895	Intermediate Similarity	NPC478182
0.7895	Intermediate Similarity	NPC90723
0.7892	Intermediate Similarity	NPC33421
0.7877	Intermediate Similarity	NPC472294
0.7874	Intermediate Similarity	NPC201634
0.7866	Intermediate Similarity	NPC314372
0.7865	Intermediate Similarity	NPC307191
0.7857	Intermediate Similarity	NPC476297
0.7853	Intermediate Similarity	NPC190296
0.784	Intermediate Similarity	NPC279081
0.784	Intermediate Similarity	NPC2949
0.7831	Intermediate Similarity	NPC317701
0.7829	Intermediate Similarity	NPC472123
0.7818	Intermediate Similarity	NPC143872
0.7816	Intermediate Similarity	NPC194411
0.7809	Intermediate Similarity	NPC314919
0.7791	Intermediate Similarity	NPC478184
0.7791	Intermediate Similarity	NPC271797
0.7791	Intermediate Similarity	NPC21174
0.7785	Intermediate Similarity	NPC82295
0.7784	Intermediate Similarity	NPC105818
0.7784	Intermediate Similarity	NPC24678
0.7772	Intermediate Similarity	NPC316018
0.7772	Intermediate Similarity	NPC315617
0.7772	Intermediate Similarity	NPC314058
0.7772	Intermediate Similarity	NPC316359
0.7758	Intermediate Similarity	NPC204141
0.773	Intermediate Similarity	NPC230002
0.7727	Intermediate Similarity	NPC161861
0.7719	Intermediate Similarity	NPC293487
0.7719	Intermediate Similarity	NPC477591
0.7702	Intermediate Similarity	NPC218268
0.7701	Intermediate Similarity	NPC56233
0.7692	Intermediate Similarity	NPC469763
0.7692	Intermediate Similarity	NPC25008
0.7692	Intermediate Similarity	NPC469760
0.7692	Intermediate Similarity	NPC259644
0.7692	Intermediate Similarity	NPC469786
0.7692	Intermediate Similarity	NPC73952
0.7692	Intermediate Similarity	NPC469765
0.7692	Intermediate Similarity	NPC200214
0.7685	Intermediate Similarity	NPC314954
0.7684	Intermediate Similarity	NPC37423
0.7684	Intermediate Similarity	NPC275305
0.7673	Intermediate Similarity	NPC475450
0.7667	Intermediate Similarity	NPC191415
0.7665	Intermediate Similarity	NPC471957
0.7657	Intermediate Similarity	NPC63751
0.7656	Intermediate Similarity	NPC475288
0.7654	Intermediate Similarity	NPC150259
0.7653	Intermediate Similarity	NPC473757
0.7651	Intermediate Similarity	NPC470440
0.7651	Intermediate Similarity	NPC159856
0.7647	Intermediate Similarity	NPC80597
0.7647	Intermediate Similarity	NPC211572
0.7647	Intermediate Similarity	NPC70922
0.7647	Intermediate Similarity	NPC212376
0.7647	Intermediate Similarity	NPC75540
0.7625	Intermediate Similarity	NPC473930
0.7614	Intermediate Similarity	NPC250835
0.7611	Intermediate Similarity	NPC16659
0.761	Intermediate Similarity	NPC22079
0.761	Intermediate Similarity	NPC475428
0.76	Intermediate Similarity	NPC474561
0.76	Intermediate Similarity	NPC49954
0.76	Intermediate Similarity	NPC478183
0.76	Intermediate Similarity	NPC160105
0.7598	Intermediate Similarity	NPC68354
0.7596	Intermediate Similarity	NPC94752
0.7582	Intermediate Similarity	NPC284678
0.7581	Intermediate Similarity	NPC324149
0.758	Intermediate Similarity	NPC250361
0.7576	Intermediate Similarity	NPC472027
0.7558	Intermediate Similarity	NPC167635
0.7558	Intermediate Similarity	NPC193740
0.7557	Intermediate Similarity	NPC317430
0.7556	Intermediate Similarity	NPC176199
0.7556	Intermediate Similarity	NPC265710
0.7556	Intermediate Similarity	NPC215795
0.7547	Intermediate Similarity	NPC473587
0.7544	Intermediate Similarity	NPC34844
0.7529	Intermediate Similarity	NPC478185
0.7529	Intermediate Similarity	NPC470823
0.7527	Intermediate Similarity	NPC48938
0.7527	Intermediate Similarity	NPC102755
0.7514	Intermediate Similarity	NPC91895
0.7514	Intermediate Similarity	NPC321708
0.7514	Intermediate Similarity	NPC213629
0.7513	Intermediate Similarity	NPC475070
0.75	Intermediate Similarity	NPC473380
0.75	Intermediate Similarity	NPC51054
0.75	Intermediate Similarity	NPC240088
0.75	Intermediate Similarity	NPC469785
0.75	Intermediate Similarity	NPC69914
0.75	Intermediate Similarity	NPC473310
0.7486	Intermediate Similarity	NPC108011
0.7485	Intermediate Similarity	NPC141926
0.7484	Intermediate Similarity	NPC473762
0.7471	Intermediate Similarity	NPC255229
0.7471	Intermediate Similarity	NPC81229
0.7463	Intermediate Similarity	NPC476492
0.7458	Intermediate Similarity	NPC201700
0.7457	Intermediate Similarity	NPC469762
0.7453	Intermediate Similarity	NPC179365
0.744	Intermediate Similarity	NPC86288
0.7438	Intermediate Similarity	NPC476131
0.7432	Intermediate Similarity	NPC139291
0.7432	Intermediate Similarity	NPC472108
0.743	Intermediate Similarity	NPC314603
0.7429	Intermediate Similarity	NPC282231
0.7427	Intermediate Similarity	NPC216713
0.7416	Intermediate Similarity	NPC32534
0.7411	Intermediate Similarity	NPC167860
0.7411	Intermediate Similarity	NPC123976
0.7405	Intermediate Similarity	NPC62749
0.7403	Intermediate Similarity	NPC284775
0.7401	Intermediate Similarity	NPC49217
0.74	Intermediate Similarity	NPC251936
0.7398	Intermediate Similarity	NPC87755
0.7396	Intermediate Similarity	NPC205254
0.7396	Intermediate Similarity	NPC23420
0.7396	Intermediate Similarity	NPC303820

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 NPC280852 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	442
0.1-0.2	689
0.2-0.3	1201
0.3-0.4	2188
0.4-0.5	2046
0.5-0.6	1677
0.6-0.7	717
0.7-0.8	178
0.8-0.85	12
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8647	High Similarity	NPD6277	Clinical (unspecified phase)
0.8571	High Similarity	NPD2837	Discontinued
0.8434	Intermediate Similarity	NPD3323	Discontinued
0.8354	Intermediate Similarity	NPD1722	Approved
0.8272	Intermediate Similarity	NPD4374	Clinical (unspecified phase)
0.8263	Intermediate Similarity	NPD1853	Clinical (unspecified phase)
0.8228	Intermediate Similarity	NPD786	Approved
0.8187	Intermediate Similarity	NPD4637	Clinical (unspecified phase)
0.8136	Intermediate Similarity	NPD6610	Clinical (unspecified phase)
0.811	Intermediate Similarity	NPD2172	Phase 1
0.8103	Intermediate Similarity	NPD4181	Approved
0.8098	Intermediate Similarity	NPD4547	Phase 3
0.8049	Intermediate Similarity	NPD3100	Discontinued
0.8038	Intermediate Similarity	NPD198	Clinical (unspecified phase)
0.8036	Intermediate Similarity	NPD5418	Discontinued
0.7977	Intermediate Similarity	NPD3609	Approved
0.7977	Intermediate Similarity	NPD3610	Approved
0.7966	Intermediate Similarity	NPD1895	Discontinued
0.7965	Intermediate Similarity	NPD4779	Clinical (unspecified phase)
0.791	Intermediate Similarity	NPD6595	Phase 3
0.7898	Intermediate Similarity	NPD6203	Clinical (unspecified phase)
0.7898	Intermediate Similarity	NPD7111	Discontinued
0.7886	Intermediate Similarity	NPD4128	Approved
0.7865	Intermediate Similarity	NPD4649	Clinical (unspecified phase)
0.7861	Intermediate Similarity	NPD2390	Clinical (unspecified phase)
0.7853	Intermediate Similarity	NPD3341	Clinical (unspecified phase)
0.784	Intermediate Similarity	NPD3943	Clinical (unspecified phase)
0.7834	Intermediate Similarity	NPD715	Phase 3
0.7818	Intermediate Similarity	NPD1683	Approved
0.7799	Intermediate Similarity	NPD3385	Approved
0.779	Intermediate Similarity	NPD2793	Discontinued
0.7784	Intermediate Similarity	NPD5065	Approved
0.7759	Intermediate Similarity	NPD2185	Clinical (unspecified phase)
0.7759	Intermediate Similarity	NPD2640	Approved
0.7759	Intermediate Similarity	NPD2641	Approved
0.7751	Intermediate Similarity	NPD975	Approved
0.7751	Intermediate Similarity	NPD977	Approved
0.7751	Intermediate Similarity	NPD976	Approved
0.7747	Intermediate Similarity	NPD7394	Phase 2
0.7742	Intermediate Similarity	NPD6278	Clinical (unspecified phase)
0.7742	Intermediate Similarity	NPD2960	Clinical (unspecified phase)
0.7711	Intermediate Similarity	NPD7469	Discontinued
0.7701	Intermediate Similarity	NPD2642	Approved
0.7701	Intermediate Similarity	NPD2639	Approved
0.7697	Intermediate Similarity	NPD1918	Clinical (unspecified phase)
0.7697	Intermediate Similarity	NPD5254	Discontinued
0.7692	Intermediate Similarity	NPD6217	Discontinued
0.7663	Intermediate Similarity	NPD5145	Clinical (unspecified phase)
0.7654	Intermediate Similarity	NPD2930	Clinical (unspecified phase)
0.765	Intermediate Similarity	NPD3961	Discontinued
0.765	Intermediate Similarity	NPD3486	Clinical (unspecified phase)
0.7644	Intermediate Similarity	NPD5744	Clinical (unspecified phase)
0.7643	Intermediate Similarity	NPD2118	Approved
0.7643	Intermediate Similarity	NPD2119	Approved
0.764	Intermediate Similarity	NPD4075	Phase 2
0.7636	Intermediate Similarity	NPD2006	Phase 2
0.7627	Intermediate Similarity	NPD7217	Approved
0.7627	Intermediate Similarity	NPD7216	Approved
0.7624	Intermediate Similarity	NPD5105	Approved
0.7624	Intermediate Similarity	NPD5106	Approved
0.7619	Intermediate Similarity	NPD2430	Phase 2
0.761	Intermediate Similarity	NPD3475	Approved
0.761	Intermediate Similarity	NPD3476	Approved
0.7606	Intermediate Similarity	NPD5462	Discontinued
0.7598	Intermediate Similarity	NPD3506	Approved
0.7598	Intermediate Similarity	NPD3505	Approved
0.7596	Intermediate Similarity	NPD3378	Clinical (unspecified phase)
0.7579	Intermediate Similarity	NPD6816	Phase 3
0.7578	Intermediate Similarity	NPD3944	Approved
0.7578	Intermediate Similarity	NPD3942	Approved
0.7562	Intermediate Similarity	NPD803	Phase 1
0.7557	Intermediate Similarity	NPD5069	Clinical (unspecified phase)
0.7556	Intermediate Similarity	NPD4076	Approved
0.7556	Intermediate Similarity	NPD4079	Approved
0.7546	Intermediate Similarity	NPD6554	Approved
0.7546	Intermediate Similarity	NPD45	Approved
0.753	Intermediate Similarity	NPD2007	Clinical (unspecified phase)
0.7529	Intermediate Similarity	NPD6771	Discontinued
0.7529	Intermediate Similarity	NPD5315	Discontinued
0.7514	Intermediate Similarity	NPD5436	Phase 1
0.7514	Intermediate Similarity	NPD4184	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD7618	Phase 3
0.75	Intermediate Similarity	NPD4426	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD7619	Phase 3
0.75	Intermediate Similarity	NPD2580	Discontinued
0.7486	Intermediate Similarity	NPD7564	Discontinued
0.7473	Intermediate Similarity	NPD1708	Approved
0.7473	Intermediate Similarity	NPD1707	Approved
0.7472	Intermediate Similarity	NPD6827	Clinical (unspecified phase)
0.7472	Intermediate Similarity	NPD6828	Phase 2
0.7471	Intermediate Similarity	NPD1403	Approved
0.7471	Intermediate Similarity	NPD6454	Clinical (unspecified phase)
0.7471	Intermediate Similarity	NPD1404	Approved
0.7469	Intermediate Similarity	NPD4028	Approved
0.7469	Intermediate Similarity	NPD4029	Approved
0.7469	Intermediate Similarity	NPD4030	Approved
0.7461	Intermediate Similarity	NPD4886	Phase 2
0.7459	Intermediate Similarity	NPD8431	Approved
0.7458	Intermediate Similarity	NPD2333	Discontinued
0.7444	Intermediate Similarity	NPD3348	Phase 2
0.7432	Intermediate Similarity	NPD1332	Clinical (unspecified phase)
0.743	Intermediate Similarity	NPD4112	Clinical (unspecified phase)
0.7424	Intermediate Similarity	NPD8458	Clinical (unspecified phase)
0.7421	Intermediate Similarity	NPD2880	Discontinued
0.7421	Intermediate Similarity	NPD991	Phase 2
0.7421	Intermediate Similarity	NPD992	Clinical (unspecified phase)
0.7418	Intermediate Similarity	NPD5962	Phase 2
0.7409	Intermediate Similarity	NPD3015	Discontinued
0.7401	Intermediate Similarity	NPD2478	Clinical (unspecified phase)
0.7391	Intermediate Similarity	NPD6178	Phase 3
0.7387	Intermediate Similarity	NPD8488	Clinical (unspecified phase)
0.7374	Intermediate Similarity	NPD1567	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD4462	Approved
0.7368	Intermediate Similarity	NPD4463	Approved
0.7366	Intermediate Similarity	NPD5590	Clinical (unspecified phase)
0.7345	Intermediate Similarity	NPD1313	Approved
0.734	Intermediate Similarity	NPD3419	Clinical (unspecified phase)
0.7337	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD1262	Discovery
0.7329	Intermediate Similarity	NPD3654	Approved
0.7326	Intermediate Similarity	NPD8110	Clinical (unspecified phase)
0.7322	Intermediate Similarity	NPD8464	Clinical (unspecified phase)
0.7312	Intermediate Similarity	NPD4902	Discontinued
0.7308	Intermediate Similarity	NPD2144	Approved
0.7304	Intermediate Similarity	NPD6615	Clinical (unspecified phase)
0.7302	Intermediate Similarity	NPD4615	Phase 2
0.7299	Intermediate Similarity	NPD3113	Approved
0.7299	Intermediate Similarity	NPD3112	Approved
0.7299	Intermediate Similarity	NPD3114	Approved
0.7299	Intermediate Similarity	NPD3115	Approved
0.7283	Intermediate Similarity	NPD3038	Discontinued
0.7282	Intermediate Similarity	NPD2364	Suspended
0.7277	Intermediate Similarity	NPD7023	Clinical (unspecified phase)
0.7277	Intermediate Similarity	NPD2316	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD1253	Approved
0.7273	Intermediate Similarity	NPD2310	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD1256	Approved
0.7273	Intermediate Similarity	NPD1254	Approved
0.7273	Intermediate Similarity	NPD1255	Approved
0.7259	Intermediate Similarity	NPD6838	Clinical (unspecified phase)
0.7259	Intermediate Similarity	NPD8493	Clinical (unspecified phase)
0.7257	Intermediate Similarity	NPD2865	Clinical (unspecified phase)
0.7257	Intermediate Similarity	NPD1192	Clinical (unspecified phase)
0.7257	Intermediate Similarity	NPD6497	Approved
0.7253	Intermediate Similarity	NPD2406	Clinical (unspecified phase)
0.7253	Intermediate Similarity	NPD6375	Clinical (unspecified phase)
0.7253	Intermediate Similarity	NPD2751	Phase 1
0.7249	Intermediate Similarity	NPD6180	Clinical (unspecified phase)
0.7247	Intermediate Similarity	NPD1333	Phase 3
0.7246	Intermediate Similarity	NPD768	Clinical (unspecified phase)
0.7245	Intermediate Similarity	NPD6288	Clinical (unspecified phase)
0.7245	Intermediate Similarity	NPD5426	Phase 3
0.7241	Intermediate Similarity	NPD2165	Phase 1
0.724	Intermediate Similarity	NPD6664	Approved
0.7232	Intermediate Similarity	NPD1016	Phase 2
0.7232	Intermediate Similarity	NPD2385	Clinical (unspecified phase)
0.7232	Intermediate Similarity	NPD1015	Phase 2
0.7222	Intermediate Similarity	NPD7666	Phase 3
0.7222	Intermediate Similarity	NPD2875	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD7665	Phase 2
0.7219	Intermediate Similarity	NPD4047	Discontinued
0.7208	Intermediate Similarity	NPD4023	Clinical (unspecified phase)
0.7204	Intermediate Similarity	NPD5892	Approved
0.7204	Intermediate Similarity	NPD3607	Clinical (unspecified phase)
0.7204	Intermediate Similarity	NPD4957	Phase 2
0.72	Intermediate Similarity	NPD2150	Discontinued
0.72	Intermediate Similarity	NPD2927	Phase 3
0.72	Intermediate Similarity	NPD473	Clinical (unspecified phase)
0.7198	Intermediate Similarity	NPD3859	Clinical (unspecified phase)
0.7189	Intermediate Similarity	NPD5806	Clinical (unspecified phase)
0.7182	Intermediate Similarity	NPD5934	Clinical (unspecified phase)
0.7172	Intermediate Similarity	NPD7445	Phase 1
0.7167	Intermediate Similarity	NPD4639	Approved
0.7167	Intermediate Similarity	NPD4640	Approved
0.7167	Intermediate Similarity	NPD4638	Approved
0.7166	Intermediate Similarity	NPD4298	Clinical (unspecified phase)
0.7165	Intermediate Similarity	NPD7621	Clinical (unspecified phase)
0.7164	Intermediate Similarity	NPD2411	Approved
0.7164	Intermediate Similarity	NPD4352	Phase 1
0.7164	Intermediate Similarity	NPD7594	Clinical (unspecified phase)
0.7159	Intermediate Similarity	NPD5300	Clinical (unspecified phase)
0.7159	Intermediate Similarity	NPD4326	Phase 2
0.7152	Intermediate Similarity	NPD270	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD271	Approved
0.7152	Intermediate Similarity	NPD268	Approved
0.7151	Intermediate Similarity	NPD1661	Suspended
0.715	Intermediate Similarity	NPD3830	Phase 1
0.7143	Intermediate Similarity	NPD2071	Approved
0.7143	Intermediate Similarity	NPD2068	Approved
0.7143	Intermediate Similarity	NPD2075	Approved
0.7143	Intermediate Similarity	NPD2074	Approved
0.7143	Intermediate Similarity	NPD6285	Phase 2
0.7143	Intermediate Similarity	NPD2072	Approved
0.7143	Intermediate Similarity	NPD2073	Approved
0.7143	Intermediate Similarity	NPD2070	Approved
0.7143	Intermediate Similarity	NPD2069	Approved
0.7136	Intermediate Similarity	NPD2443	Approved
0.7136	Intermediate Similarity	NPD2442	Approved
0.7136	Intermediate Similarity	NPD6459	Phase 2
0.7135	Intermediate Similarity	NPD5473	Discontinued

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