NPASS Compound

Structure

NPC5180 OpenBabel07101718312D 34 39 0 0 1 0 0 0 0 0999 V2000 2.3038 -4.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3002 -0.3709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8533 -3.4589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6672 -3.3917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8060 -4.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0762 -2.1095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3239 -3.5659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0519 -1.2968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9117 -4.3749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5638 -2.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 -3.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3729 -4.8749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6128 -3.5962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3729 -3.8749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5638 -3.2872 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6128 -1.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2079 -2.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4559 -2.6353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0739 -4.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0250 -2.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 -0.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6581 -1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0739 -1.4781 0.0000 C 0 0 2 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 -1.4013 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6581 -2.4781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0739 -2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7075 -3.6031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0739 -5.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4945 0.9706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9400 -3.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3239 -5.1840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0250 -1.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 5 31 1 0 0 0 0 6 8 2 0 0 0 0 6 18 1 0 0 0 0 7 9 2 0 0 0 0 7 14 1 0 0 0 0 8 25 1 0 0 0 0 9 32 1 0 0 0 0 10 15 1 0 0 0 0 11 17 1 0 0 0 0 11 19 1 0 0 0 0 12 14 2 0 0 0 0 12 32 1 0 0 0 0 13 15 1 0 0 0 0 13 20 2 0 0 0 0 15 14 1 1 0 0 0 16 10 1 6 0 0 0 16 20 1 0 0 0 0 16 33 1 0 0 0 0 17 26 1 6 0 0 0 17 27 1 0 0 0 0 18 26 1 0 0 0 0 18 28 2 0 0 0 0 19 29 2 0 0 0 0 19 31 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 34 1 1 0 0 0 22 25 1 6 0 0 0 22 26 1 0 0 0 0 23 27 1 1 0 0 0 23 33 1 0 0 0 0 24 25 1 0 0 0 0 24 30 2 0 0 0 0 24 34 1 0 0 0 0 25 2 1 6 0 0 0 26 3 1 6 0 0 0 27 4 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	308.24
Volume:	347.085
LogP:	5.96
LogD:	4.015
LogS:	-4.457
# Rotatable Bonds:	12
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.312
Synthetic Accessibility Score:	3.35
Fsp3:	0.737
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.923
MDCK Permeability:	2.5098166588577442e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.924
Plasma Protein Binding (PPB):	97.4166488647461%
Volume Distribution (VD):	0.893
Pgp-substrate:	1.7446478605270386%

ADMET: Metabolism

CYP1A2-inhibitor:	0.384
CYP1A2-substrate:	0.164
CYP2C19-inhibitor:	0.552
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.306
CYP2C9-substrate:	0.835
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.059
CYP3A4-inhibitor:	0.325
CYP3A4-substrate:	0.104

ADMET: Excretion

Clearance (CL):	5.263
Half-life (T1/2):	0.148

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.033
Drug-inuced Liver Injury (DILI):	0.284
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.554
Maximum Recommended Daily Dose:	0.988
Skin Sensitization:	0.979
Carcinogencity:	0.575
Eye Corrosion:	0.988
Eye Irritation:	0.975
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC5180

Natural Product ID:	NPC5180
*Common Name:**	Nimbolide
IUPAC Name:	n.a.
Synonyms:	Nimbolide
Standard InCHIKey:	JZIQWNPPBKFOPT-LSYMHUITSA-N
Standard InCHI:	InChI=1S/C27H30O7/c1-13-15(14-7-9-32-12-14)10-16-20(13)27(4)17(11-19(29)31-5)26(3)18(28)6-8-25(2)22(26)21(23(27)33-16)34-24(25)30/h6-9,12,15-17,21-23H,10-11H2,1-5H3/t15-,16-,17-,21-,22+,23-,25-,26+,27-/m1/s1
SMILES:	COC(=O)C[C@H]1[C@@]2(C)[C@H](O[C@H]3C2=C(C)[C@@H](C3)c2cocc2)[C@H]2[C@@H]3[C@]1(C)C(=O)C=C[C@@]3(C)C(=O)O2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL426690
PubChem CID:	12313376
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids [CHEMONTID:0002380] Limonoids

*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
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193038]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1593280]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18816111]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	fruits	n.a.	n.a.	PMID[20669933]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[21381696]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381696]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2607354]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614419]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26339153]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28493718]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	Eukaryota	n.a.	bark	n.a.	PMID[9134742]
NPO4406	Azadirachta indica	Species	Meliaceae	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
EC50	1
ED50	7
IC50	9
Others	3

Activity Type	# Activity
Cell Line	14
NON-MOLECULAR	1
Organism	3
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT382	Cell Line	OVCAR-5	Homo sapiens	IC50	=	4170.0	nM	PMID[520781]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	4590.0	nM	PMID[520781]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	15560.0	nM	PMID[520781]
NPT379	Cell Line	HOP-62	Homo sapiens	IC50	=	10370.0	nM	PMID[520781]
NPT6349	Cell Line	SW-60	Homo sapiens	IC50	=	8250.0	nM	PMID[520781]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	6940.0	nM	PMID[520781]
NPT1851	Cell Line	Col2	Homo sapiens	ED50	=	0.41	ug ml-1	PMID[520783]
NPT453	Cell Line	HT-1080	Homo sapiens	ED50	=	0.31	ug ml-1	PMID[520783]
NPT1034	Cell Line	Lu1	Homo sapiens	ED50	=	0.42	ug ml-1	PMID[520783]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	0.53	ug ml-1	PMID[520783]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	0.25	ug ml-1	PMID[520783]
NPT168	Cell Line	P388	Mus musculus	ED50	=	0.065	ug ml-1	PMID[520783]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	6000.0	nM	PMID[520786]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	4000.0	nM	PMID[520786]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1.74	ug.mL-1	PMID[520782]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	=	0.39	ug ml-1	PMID[520783]
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	EC50	=	0.00095	ug.mL-1	PMID[520784]
NPT1175	Organism	Spodoptera litura	Spodoptera litura	AFI	=	37.0	%	PMID[520785]
NPT27	Others	Unspecified		Cmax	=	0.0153	ug.mL-1	PMID[520786]
NPT27	Others	Unspecified		Cmax	=	5.555	ug.mL-1	PMID[520786]

☑ 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 NPC5180 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	386
0.1-0.2	1441
0.2-0.3	3179
0.3-0.4	6601
0.4-0.5	12061
0.5-0.6	10101
0.6-0.7	7905
0.7-0.8	769
0.8-0.85	206
0.85-0.9	32
0.9-0.95	13
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.993	High Similarity	NPC291150
0.9655	High Similarity	NPC116717
0.9384	High Similarity	NPC471001
0.9333	High Similarity	NPC197137
0.9195	High Similarity	NPC322546
0.9195	High Similarity	NPC308205
0.9195	High Similarity	NPC471002
0.9178	High Similarity	NPC470999
0.911	High Similarity	NPC34056
0.9079	High Similarity	NPC470118
0.9073	High Similarity	NPC296807
0.9073	High Similarity	NPC141538
0.9073	High Similarity	NPC155939
0.9	High Similarity	NPC471000
0.8954	High Similarity	NPC214495
0.8954	High Similarity	NPC469847
0.8954	High Similarity	NPC470119
0.8947	High Similarity	NPC92979
0.894	High Similarity	NPC29695
0.894	High Similarity	NPC182427
0.8912	High Similarity	NPC199044
0.8912	High Similarity	NPC238843
0.8816	High Similarity	NPC470996
0.8808	High Similarity	NPC196846
0.8792	High Similarity	NPC471292
0.8782	High Similarity	NPC471003
0.8774	High Similarity	NPC475226
0.8767	High Similarity	NPC56197
0.875	High Similarity	NPC272590
0.875	High Similarity	NPC285227
0.8742	High Similarity	NPC234494
0.8733	High Similarity	NPC471174
0.8726	High Similarity	NPC471168
0.8718	High Similarity	NPC191828
0.8716	High Similarity	NPC223415
0.8716	High Similarity	NPC470741
0.871	High Similarity	NPC475066
0.8671	High Similarity	NPC61967
0.8658	High Similarity	NPC251865
0.8654	High Similarity	NPC472671
0.8627	High Similarity	NPC18135
0.8618	High Similarity	NPC195325
0.8609	High Similarity	NPC71821
0.8609	High Similarity	NPC216755
0.8609	High Similarity	NPC302987
0.8581	High Similarity	NPC20500
0.8581	High Similarity	NPC471175
0.8571	High Similarity	NPC33938
0.8571	High Similarity	NPC268905
0.8571	High Similarity	NPC246164
0.8562	High Similarity	NPC469335
0.8562	High Similarity	NPC156189
0.8562	High Similarity	NPC159927
0.8562	High Similarity	NPC470997
0.8544	High Similarity	NPC471166
0.8544	High Similarity	NPC471167
0.8544	High Similarity	NPC470792
0.8531	High Similarity	NPC298190
0.8526	High Similarity	NPC175964
0.8526	High Similarity	NPC471169
0.8516	High Similarity	NPC34421
0.8516	High Similarity	NPC237259
0.8516	High Similarity	NPC98206
0.8497	Intermediate Similarity	NPC472654
0.8487	Intermediate Similarity	NPC221809
0.8487	Intermediate Similarity	NPC255414
0.8477	Intermediate Similarity	NPC185456
0.8471	Intermediate Similarity	NPC167142
0.8471	Intermediate Similarity	NPC472283
0.8467	Intermediate Similarity	NPC80635
0.8466	Intermediate Similarity	NPC469848
0.8462	Intermediate Similarity	NPC44675
0.8462	Intermediate Similarity	NPC264943
0.8462	Intermediate Similarity	NPC214541
0.8452	Intermediate Similarity	NPC75906
0.8446	Intermediate Similarity	NPC90953
0.8442	Intermediate Similarity	NPC196864
0.8442	Intermediate Similarity	NPC477404
0.8438	Intermediate Similarity	NPC126984
0.8438	Intermediate Similarity	NPC27541
0.8438	Intermediate Similarity	NPC62692
0.8431	Intermediate Similarity	NPC471007
0.8428	Intermediate Similarity	NPC197596
0.8428	Intermediate Similarity	NPC472668
0.8418	Intermediate Similarity	NPC84349
0.8414	Intermediate Similarity	NPC471006
0.8408	Intermediate Similarity	NPC204663
0.8408	Intermediate Similarity	NPC60973
0.84	Intermediate Similarity	NPC121158
0.8397	Intermediate Similarity	NPC178932
0.8385	Intermediate Similarity	NPC307781
0.8385	Intermediate Similarity	NPC472670
0.8378	Intermediate Similarity	NPC236532
0.8377	Intermediate Similarity	NPC69647
0.8377	Intermediate Similarity	NPC470791
0.8377	Intermediate Similarity	NPC470790
0.8377	Intermediate Similarity	NPC125182
0.8375	Intermediate Similarity	NPC285567
0.8375	Intermediate Similarity	NPC419
0.8375	Intermediate Similarity	NPC224394
0.8375	Intermediate Similarity	NPC283209
0.8375	Intermediate Similarity	NPC663
0.8375	Intermediate Similarity	NPC292389
0.8375	Intermediate Similarity	NPC472669
0.8375	Intermediate Similarity	NPC469338
0.8367	Intermediate Similarity	NPC146872
0.8365	Intermediate Similarity	NPC287559
0.8365	Intermediate Similarity	NPC305016
0.8354	Intermediate Similarity	NPC472778
0.8354	Intermediate Similarity	NPC299038
0.8354	Intermediate Similarity	NPC472777
0.8354	Intermediate Similarity	NPC195131
0.8354	Intermediate Similarity	NPC472776
0.8354	Intermediate Similarity	NPC261597
0.8344	Intermediate Similarity	NPC469850
0.8344	Intermediate Similarity	NPC469336
0.8344	Intermediate Similarity	NPC25351
0.8333	Intermediate Similarity	NPC476201
0.8333	Intermediate Similarity	NPC294511
0.8333	Intermediate Similarity	NPC476224
0.8333	Intermediate Similarity	NPC472672
0.8333	Intermediate Similarity	NPC121615
0.8333	Intermediate Similarity	NPC472764
0.8323	Intermediate Similarity	NPC470940
0.8323	Intermediate Similarity	NPC476936
0.8323	Intermediate Similarity	NPC228842
0.8323	Intermediate Similarity	NPC469849
0.8323	Intermediate Similarity	NPC276551
0.8313	Intermediate Similarity	NPC5741
0.8313	Intermediate Similarity	NPC18986
0.8313	Intermediate Similarity	NPC478177
0.8313	Intermediate Similarity	NPC472771
0.8313	Intermediate Similarity	NPC69028
0.8311	Intermediate Similarity	NPC470742
0.8302	Intermediate Similarity	NPC474932
0.8302	Intermediate Similarity	NPC477403
0.8302	Intermediate Similarity	NPC475967
0.8293	Intermediate Similarity	NPC475641
0.8293	Intermediate Similarity	NPC475237
0.8291	Intermediate Similarity	NPC209364
0.8291	Intermediate Similarity	NPC104736
0.8291	Intermediate Similarity	NPC263265
0.8282	Intermediate Similarity	NPC472766
0.8282	Intermediate Similarity	NPC472765
0.8282	Intermediate Similarity	NPC327922
0.828	Intermediate Similarity	NPC302054
0.828	Intermediate Similarity	NPC57998
0.828	Intermediate Similarity	NPC253201
0.8278	Intermediate Similarity	NPC473152
0.8272	Intermediate Similarity	NPC472141
0.8272	Intermediate Similarity	NPC470875
0.8267	Intermediate Similarity	NPC148374
0.8261	Intermediate Similarity	NPC476197
0.8261	Intermediate Similarity	NPC472773
0.8261	Intermediate Similarity	NPC165218
0.8258	Intermediate Similarity	NPC470998
0.825	Intermediate Similarity	NPC477402
0.8247	Intermediate Similarity	NPC250228
0.8239	Intermediate Similarity	NPC286722
0.8239	Intermediate Similarity	NPC187149
0.8239	Intermediate Similarity	NPC36655
0.8239	Intermediate Similarity	NPC304692
0.8235	Intermediate Similarity	NPC56731
0.8232	Intermediate Similarity	NPC118086
0.8228	Intermediate Similarity	NPC476262
0.8224	Intermediate Similarity	NPC267632
0.8224	Intermediate Similarity	NPC243577
0.8221	Intermediate Similarity	NPC478179
0.8221	Intermediate Similarity	NPC476850
0.8221	Intermediate Similarity	NPC173516
0.8221	Intermediate Similarity	NPC476861
0.8219	Intermediate Similarity	NPC471817
0.8217	Intermediate Similarity	NPC84063
0.821	Intermediate Similarity	NPC123088
0.8199	Intermediate Similarity	NPC470939
0.8199	Intermediate Similarity	NPC6326
0.8199	Intermediate Similarity	NPC472767
0.8199	Intermediate Similarity	NPC329938
0.8199	Intermediate Similarity	NPC68848
0.8193	Intermediate Similarity	NPC94763
0.8193	Intermediate Similarity	NPC236004
0.8188	Intermediate Similarity	NPC310043
0.8188	Intermediate Similarity	NPC310830
0.8187	Intermediate Similarity	NPC307383
0.8187	Intermediate Similarity	NPC475295
0.8187	Intermediate Similarity	NPC473473
0.8187	Intermediate Similarity	NPC237155
0.8182	Intermediate Similarity	NPC346
0.8182	Intermediate Similarity	NPC262198
0.8176	Intermediate Similarity	NPC92941
0.8176	Intermediate Similarity	NPC469485
0.8176	Intermediate Similarity	NPC242068
0.8176	Intermediate Similarity	NPC158525
0.8176	Intermediate Similarity	NPC107646
0.8176	Intermediate Similarity	NPC247563
0.8171	Intermediate Similarity	NPC472673
0.8171	Intermediate Similarity	NPC471397
0.817	Intermediate Similarity	NPC142113
0.817	Intermediate Similarity	NPC84479
0.8165	Intermediate Similarity	NPC30222

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 NPC5180 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	324
0.1-0.2	1008
0.2-0.3	2197
0.3-0.4	2747
0.4-0.5	1911
0.5-0.6	763
0.6-0.7	190
0.7-0.8	10
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
0.7914	Intermediate Similarity	NPD5537	Clinical (unspecified phase)
0.7888	Intermediate Similarity	NPD5760	Phase 2
0.7888	Intermediate Similarity	NPD5761	Phase 2
0.7719	Intermediate Similarity	NPD6764	Approved
0.7719	Intermediate Similarity	NPD6765	Approved
0.76	Intermediate Similarity	NPD8434	Phase 2
0.7543	Intermediate Similarity	NPD6785	Approved
0.7543	Intermediate Similarity	NPD6784	Approved
0.7358	Intermediate Similarity	NPD4628	Phase 3
0.717	Intermediate Similarity	NPD1471	Phase 3
0.7091	Intermediate Similarity	NPD920	Approved
0.7081	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7076	Intermediate Similarity	NPD919	Approved
0.7063	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.703	Intermediate Similarity	NPD6273	Approved
0.6994	Remote Similarity	NPD1247	Approved
0.6989	Remote Similarity	NPD7893	Clinical (unspecified phase)
0.697	Remote Similarity	NPD642	Clinical (unspecified phase)
0.6964	Remote Similarity	NPD6599	Discontinued
0.6951	Remote Similarity	NPD643	Clinical (unspecified phase)
0.6936	Remote Similarity	NPD5494	Approved
0.6805	Remote Similarity	NPD3226	Approved
0.68	Remote Similarity	NPD8127	Discontinued
0.6789	Remote Similarity	NPD4107	Approved
0.6768	Remote Similarity	NPD1243	Approved
0.6744	Remote Similarity	NPD7819	Suspended
0.6744	Remote Similarity	NPD7096	Clinical (unspecified phase)
0.673	Remote Similarity	NPD8032	Phase 2
0.6728	Remote Similarity	NPD3748	Approved
0.6728	Remote Similarity	NPD2799	Discontinued
0.6711	Remote Similarity	NPD17	Approved
0.6707	Remote Similarity	NPD6799	Approved
0.6706	Remote Similarity	NPD7458	Discontinued
0.6688	Remote Similarity	NPD3972	Approved
0.6687	Remote Similarity	NPD2796	Approved
0.6686	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD8055	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD4482	Phase 3
0.6667	Remote Similarity	NPD6808	Phase 2
0.6667	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD5844	Phase 1
0.6648	Remote Similarity	NPD6559	Discontinued
0.6646	Remote Similarity	NPD6005	Phase 3
0.6646	Remote Similarity	NPD6003	Clinical (unspecified phase)
0.6646	Remote Similarity	NPD6004	Phase 3
0.6646	Remote Similarity	NPD6006	Clinical (unspecified phase)
0.6646	Remote Similarity	NPD6002	Phase 3
0.6629	Remote Similarity	NPD7075	Discontinued
0.6629	Remote Similarity	NPD3926	Phase 2
0.6628	Remote Similarity	NPD7411	Suspended
0.6627	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.6627	Remote Similarity	NPD4109	Clinical (unspecified phase)
0.6627	Remote Similarity	NPD4110	Phase 3
0.6607	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.659	Remote Similarity	NPD6801	Discontinued
0.6587	Remote Similarity	NPD3887	Approved
0.6581	Remote Similarity	NPD1608	Approved
0.6571	Remote Similarity	NPD4967	Phase 2
0.6571	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.6571	Remote Similarity	NPD4966	Approved
0.6571	Remote Similarity	NPD4965	Approved
0.6571	Remote Similarity	NPD3882	Suspended
0.657	Remote Similarity	NPD7028	Phase 2
0.6568	Remote Similarity	NPD2532	Approved
0.6568	Remote Similarity	NPD2534	Approved
0.6568	Remote Similarity	NPD2533	Approved
0.6561	Remote Similarity	NPD3266	Approved
0.6561	Remote Similarity	NPD3267	Approved
0.6561	Remote Similarity	NPD1049	Clinical (unspecified phase)
0.6548	Remote Similarity	NPD7236	Approved
0.6545	Remote Similarity	NPD5763	Approved
0.6545	Remote Similarity	NPD5762	Approved
0.6545	Remote Similarity	NPD2346	Discontinued
0.6545	Remote Similarity	NPD2344	Approved
0.6543	Remote Similarity	NPD6355	Discontinued
0.6535	Remote Similarity	NPD8404	Phase 2
0.6534	Remote Similarity	NPD3749	Approved
0.6527	Remote Similarity	NPD3750	Approved
0.6517	Remote Similarity	NPD7199	Phase 2
0.6514	Remote Similarity	NPD3817	Phase 2
0.6514	Remote Similarity	NPD5616	Clinical (unspecified phase)
0.6514	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6497	Remote Similarity	NPD1876	Approved
0.6497	Remote Similarity	NPD6234	Discontinued
0.6494	Remote Similarity	NPD3412	Clinical (unspecified phase)
0.6485	Remote Similarity	NPD2438	Suspended
0.6481	Remote Similarity	NPD4140	Approved
0.6467	Remote Similarity	NPD1241	Discontinued
0.6467	Remote Similarity	NPD2800	Approved
0.6464	Remote Similarity	NPD7473	Discontinued
0.646	Remote Similarity	NPD3268	Approved
0.6457	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.6444	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6438	Remote Similarity	NPD6832	Phase 2
0.6437	Remote Similarity	NPD6386	Approved
0.6437	Remote Similarity	NPD6385	Approved
0.6429	Remote Similarity	NPD2163	Approved
0.6429	Remote Similarity	NPD3818	Discontinued
0.6429	Remote Similarity	NPD7003	Approved
0.6429	Remote Similarity	NPD7799	Discontinued
0.6416	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6415	Remote Similarity	NPD5647	Approved
0.6409	Remote Similarity	NPD2403	Approved
0.6409	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6407	Remote Similarity	NPD970	Clinical (unspecified phase)
0.64	Remote Similarity	NPD37	Approved
0.64	Remote Similarity	NPD1934	Approved
0.6391	Remote Similarity	NPD2309	Approved
0.6389	Remote Similarity	NPD6232	Discontinued
0.6387	Remote Similarity	NPD1778	Approved
0.6386	Remote Similarity	NPD1551	Phase 2
0.638	Remote Similarity	NPD2979	Phase 3
0.6378	Remote Similarity	NPD3057	Approved
0.6376	Remote Similarity	NPD2181	Clinical (unspecified phase)
0.6358	Remote Similarity	NPD7239	Suspended
0.6358	Remote Similarity	NPD2313	Discontinued
0.6358	Remote Similarity	NPD6859	Clinical (unspecified phase)
0.6358	Remote Similarity	NPD3764	Approved
0.6353	Remote Similarity	NPD6652	Clinical (unspecified phase)
0.6347	Remote Similarity	NPD2355	Clinical (unspecified phase)
0.6347	Remote Similarity	NPD2353	Approved
0.6345	Remote Similarity	NPD7497	Discontinued
0.6337	Remote Similarity	NPD7314	Clinical (unspecified phase)
0.6331	Remote Similarity	NPD8166	Discontinued
0.6329	Remote Similarity	NPD5327	Phase 3
0.6328	Remote Similarity	NPD5402	Approved
0.6328	Remote Similarity	NPD5353	Approved
0.6323	Remote Similarity	NPD5585	Approved
0.6323	Remote Similarity	NPD5691	Approved
0.6316	Remote Similarity	NPD8397	Clinical (unspecified phase)
0.6312	Remote Similarity	NPD6007	Clinical (unspecified phase)
0.631	Remote Similarity	NPD1549	Phase 2
0.631	Remote Similarity	NPD8312	Approved
0.631	Remote Similarity	NPD8313	Approved
0.6307	Remote Similarity	NPD6280	Approved
0.6307	Remote Similarity	NPD6279	Approved
0.6306	Remote Similarity	NPD1281	Approved
0.6306	Remote Similarity	NPD1547	Clinical (unspecified phase)
0.6301	Remote Similarity	NPD5403	Approved
0.6296	Remote Similarity	NPD5952	Clinical (unspecified phase)
0.6294	Remote Similarity	NPD3533	Approved
0.6294	Remote Similarity	NPD2972	Approved
0.6293	Remote Similarity	NPD5980	Discovery
0.629	Remote Similarity	NPD7685	Pre-registration
0.6287	Remote Similarity	NPD6100	Approved
0.6287	Remote Similarity	NPD6099	Approved
0.6286	Remote Similarity	NPD4380	Phase 2
0.628	Remote Similarity	NPD4307	Phase 2
0.6279	Remote Similarity	NPD4378	Clinical (unspecified phase)
0.6279	Remote Similarity	NPD5401	Approved
0.6273	Remote Similarity	NPD9494	Approved
0.6271	Remote Similarity	NPD2801	Approved
0.6264	Remote Similarity	NPD5242	Approved
0.6258	Remote Similarity	NPD9545	Approved
0.6258	Remote Similarity	NPD6798	Discontinued
0.6257	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.625	Remote Similarity	NPD7177	Discontinued
0.625	Remote Similarity	NPD1550	Clinical (unspecified phase)
0.625	Remote Similarity	NPD7228	Approved
0.625	Remote Similarity	NPD6873	Phase 2
0.625	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.6242	Remote Similarity	NPD1933	Approved
0.6242	Remote Similarity	NPD1899	Clinical (unspecified phase)
0.6242	Remote Similarity	NPD5735	Approved
0.6242	Remote Similarity	NPD447	Suspended
0.6237	Remote Similarity	NPD7993	Clinical (unspecified phase)
0.623	Remote Similarity	NPD4575	Clinical (unspecified phase)
0.6228	Remote Similarity	NPD7033	Discontinued
0.622	Remote Similarity	NPD6663	Approved
0.6212	Remote Similarity	NPD2491	Approved
0.6211	Remote Similarity	NPD2798	Approved
0.6209	Remote Similarity	NPD7315	Approved
0.6209	Remote Similarity	NPD7229	Phase 3
0.6205	Remote Similarity	NPD6653	Approved
0.6201	Remote Similarity	NPD7768	Phase 2
0.6199	Remote Similarity	NPD2354	Approved
0.619	Remote Similarity	NPD2531	Phase 2
0.619	Remote Similarity	NPD2935	Discontinued
0.6188	Remote Similarity	NPD1283	Approved
0.6185	Remote Similarity	NPD3146	Approved
0.6185	Remote Similarity	NPD3688	Clinical (unspecified phase)
0.6182	Remote Similarity	NPD3140	Approved
0.6182	Remote Similarity	NPD4060	Phase 1
0.6182	Remote Similarity	NPD3142	Approved
0.618	Remote Similarity	NPD1465	Phase 2
0.6178	Remote Similarity	NPD6040	Clinical (unspecified phase)
0.6166	Remote Similarity	NPD7879	Clinical (unspecified phase)
0.6159	Remote Similarity	NPD1699	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD6959	Discontinued
0.6149	Remote Similarity	NPD2797	Approved
0.6145	Remote Similarity	NPD5978	Approved
0.6145	Remote Similarity	NPD230	Phase 1
0.6145	Remote Similarity	NPD5977	Approved
0.6142	Remote Similarity	NPD8285	Discontinued
0.6141	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.6141	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6141	Remote Similarity	NPD6166	Phase 2
0.6141	Remote Similarity	NPD4481	Phase 3
0.614	Remote Similarity	NPD1878	Clinical (unspecified phase)
0.6139	Remote Similarity	NPD7457	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