NPASS Compound

Structure

NPC469844 OpenBabel07101719252D 34 38 0 0 1 0 0 0 0 0999 V2000 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8301 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1280 -0.4523 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 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4644 1.1303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7213 0.4612 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3364 1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1226 -0.3478 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8364 2.4487 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7917 -1.0909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3305 0.6303 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 15 1 0 0 0 0 2 25 1 0 0 0 0 3 25 1 0 0 0 0 7 9 1 0 0 0 0 7 18 1 0 0 0 0 8 10 2 0 0 0 0 8 21 1 0 0 0 0 9 27 1 0 0 0 0 10 26 1 0 0 0 0 11 23 1 0 0 0 0 12 17 1 0 0 0 0 12 20 2 0 0 0 0 13 19 1 0 0 0 0 13 22 1 0 0 0 0 14 16 1 0 0 0 0 14 33 1 0 0 0 0 15 29 2 0 0 0 0 15 34 1 0 0 0 0 16 11 1 6 0 0 0 16 24 1 0 0 0 0 17 24 1 0 0 0 0 17 30 2 0 0 0 0 18 26 1 6 0 0 0 18 28 1 0 0 0 0 19 25 1 0 0 0 0 19 26 1 6 0 0 0 20 27 1 0 0 0 0 20 28 1 0 0 0 0 21 25 1 0 0 0 0 21 31 2 0 0 0 0 22 28 1 1 0 0 0 22 34 1 0 0 0 0 23 32 1 0 0 0 0 23 33 1 0 0 0 0 24 27 1 1 0 0 0 26 4 1 6 0 0 0 27 5 1 1 0 0 0 28 6 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.27
Volume:	489.621
LogP:	2.475
LogD:	1.982
LogS:	-4.501
# Rotatable Bonds:	3
TPSA:	89.9
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.614
Synthetic Accessibility Score:	5.261
Fsp3:	0.75
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.211
MDCK Permeability:	2.505290467524901e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.968
30% Bioavailability (F30%):	0.294

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.146
Plasma Protein Binding (PPB):	86.606201171875%
Volume Distribution (VD):	1.625
Pgp-substrate:	11.845807075500488%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.509
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.838
CYP2C9-inhibitor:	0.147
CYP2C9-substrate:	0.031
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.041
CYP3A4-inhibitor:	0.675
CYP3A4-substrate:	0.883

ADMET: Excretion

Clearance (CL):	2.385
Half-life (T1/2):	0.548

ADMET: Toxicity

hERG Blockers:	0.369
Human Hepatotoxicity (H-HT):	0.468
Drug-inuced Liver Injury (DILI):	0.151
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.345
Maximum Recommended Daily Dose:	0.971
Skin Sensitization:	0.957
Carcinogencity:	0.057
Eye Corrosion:	0.005
Eye Irritation:	0.03
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC469844

Natural Product ID:	NPC469844
*Common Name:**	Desmethyllimocin B
IUPAC Name:	[(5R,7R,8R,9R,10R,13S,17S)-17-[(3R)-5-hydroxyoxolan-3-yl]-4,4,8,10,13-pentamethyl-3,16-dioxo-6,7,9,11,12,17-hexahydro-5H-cyclopenta[a]phenanthren-7-yl] acetate
Synonyms:
Standard InCHIKey:	OLDRWPRIFGFBQV-JYPNLMPBSA-N
Standard InCHI:	InChI=1S/C28H38O6/c1-15(29)34-22-13-19-25(2,3)21(31)8-10-26(19,4)18-7-9-27(5)20(28(18,22)6)12-17(30)24(27)16-11-23(32)33-14-16/h8,10,12,16,18-19,22-24,32H,7,9,11,13-14H2,1-6H3/t16-,18+,19-,22+,23?,24+,26+,27+,28+/m0/s1
SMILES:	CC(=O)O[C@@H]1C[C@@H]2[C@]([C@@H]3[C@]1(C)C1=CC(=O)[C@H]([C@@]1(CC3)C)[C@@H]1COC(C1)O)(C)C=CC(=O)C2(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1214755
PubChem CID:	49864004
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.	bark	n.a.	PMID[9134742]
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.	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	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	4800.0	nM	PMID[552669]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	2590.0	nM	PMID[552669]

☑ 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 NPC469844 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	203
0.1-0.2	1240
0.2-0.3	4535
0.3-0.4	9542
0.4-0.5	11710
0.5-0.6	6477
0.6-0.7	5778
0.7-0.8	3079
0.8-0.85	113
0.85-0.9	17
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9091	High Similarity	NPC292133
0.8909	High Similarity	NPC161065
0.8857	High Similarity	NPC469845
0.8835	High Similarity	NPC264048
0.8829	High Similarity	NPC241192
0.8807	High Similarity	NPC302471
0.8692	High Similarity	NPC239097
0.8692	High Similarity	NPC5284
0.8687	High Similarity	NPC79117
0.8624	High Similarity	NPC255017
0.8598	High Similarity	NPC41405
0.8558	High Similarity	NPC136289
0.8532	High Similarity	NPC194951
0.8532	High Similarity	NPC12046
0.8468	Intermediate Similarity	NPC243981
0.8462	Intermediate Similarity	NPC81530
0.8462	Intermediate Similarity	NPC476240
0.8462	Intermediate Similarity	NPC476223
0.8462	Intermediate Similarity	NPC224720
0.8455	Intermediate Similarity	NPC157441
0.8455	Intermediate Similarity	NPC471627
0.8455	Intermediate Similarity	NPC471173
0.8447	Intermediate Similarity	NPC114274
0.8396	Intermediate Similarity	NPC189616
0.8396	Intermediate Similarity	NPC255309
0.8393	Intermediate Similarity	NPC284068
0.8365	Intermediate Similarity	NPC476274
0.8364	Intermediate Similarity	NPC152117
0.8364	Intermediate Similarity	NPC234042
0.8364	Intermediate Similarity	NPC71348
0.835	Intermediate Similarity	NPC108078
0.835	Intermediate Similarity	NPC23680
0.8349	Intermediate Similarity	NPC197428
0.8349	Intermediate Similarity	NPC470065
0.8333	Intermediate Similarity	NPC317586
0.8333	Intermediate Similarity	NPC470016
0.8318	Intermediate Similarity	NPC96377
0.8317	Intermediate Similarity	NPC170220
0.8317	Intermediate Similarity	NPC107674
0.8317	Intermediate Similarity	NPC141497
0.8317	Intermediate Similarity	NPC470224
0.8317	Intermediate Similarity	NPC470656
0.8302	Intermediate Similarity	NPC140723
0.8269	Intermediate Similarity	NPC194196
0.8252	Intermediate Similarity	NPC471039
0.8241	Intermediate Similarity	NPC44063
0.8241	Intermediate Similarity	NPC220974
0.8235	Intermediate Similarity	NPC166906
0.8235	Intermediate Similarity	NPC159410
0.8224	Intermediate Similarity	NPC235889
0.8224	Intermediate Similarity	NPC472228
0.8224	Intermediate Similarity	NPC472227
0.8218	Intermediate Similarity	NPC212301
0.8218	Intermediate Similarity	NPC86266
0.8218	Intermediate Similarity	NPC110657
0.8214	Intermediate Similarity	NPC471398
0.82	Intermediate Similarity	NPC119416
0.8173	Intermediate Similarity	NPC226986
0.8165	Intermediate Similarity	NPC275539
0.8165	Intermediate Similarity	NPC189075
0.8155	Intermediate Similarity	NPC469599
0.8151	Intermediate Similarity	NPC473620
0.8148	Intermediate Similarity	NPC181265
0.8148	Intermediate Similarity	NPC102352
0.8148	Intermediate Similarity	NPC470309
0.8142	Intermediate Similarity	NPC270958
0.8137	Intermediate Similarity	NPC267266
0.8137	Intermediate Similarity	NPC277721
0.8136	Intermediate Similarity	NPC47113
0.8136	Intermediate Similarity	NPC174367
0.8131	Intermediate Similarity	NPC132395
0.8131	Intermediate Similarity	NPC471365
0.8131	Intermediate Similarity	NPC471364
0.8125	Intermediate Similarity	NPC52634
0.8125	Intermediate Similarity	NPC25909
0.8113	Intermediate Similarity	NPC63249
0.8103	Intermediate Similarity	NPC204731
0.81	Intermediate Similarity	NPC474677
0.8095	Intermediate Similarity	NPC473154
0.8095	Intermediate Similarity	NPC478056
0.8091	Intermediate Similarity	NPC241927
0.8091	Intermediate Similarity	NPC112457
0.8091	Intermediate Similarity	NPC2766
0.8091	Intermediate Similarity	NPC258543
0.8077	Intermediate Similarity	NPC305483
0.8077	Intermediate Similarity	NPC95565
0.8077	Intermediate Similarity	NPC96859
0.8077	Intermediate Similarity	NPC328162
0.8073	Intermediate Similarity	NPC475294
0.8073	Intermediate Similarity	NPC59530
0.8073	Intermediate Similarity	NPC3316
0.8073	Intermediate Similarity	NPC96333
0.8073	Intermediate Similarity	NPC110496
0.8073	Intermediate Similarity	NPC88833
0.8073	Intermediate Similarity	NPC144854
0.8067	Intermediate Similarity	NPC298841
0.8067	Intermediate Similarity	NPC42399
0.8058	Intermediate Similarity	NPC471040
0.8058	Intermediate Similarity	NPC49670
0.8056	Intermediate Similarity	NPC101842
0.8056	Intermediate Similarity	NPC96268
0.8056	Intermediate Similarity	NPC471293
0.8037	Intermediate Similarity	NPC134077
0.8036	Intermediate Similarity	NPC69291
0.8019	Intermediate Similarity	NPC476303
0.8019	Intermediate Similarity	NPC316964
0.8019	Intermediate Similarity	NPC112167
0.8019	Intermediate Similarity	NPC88198
0.8018	Intermediate Similarity	NPC101450
0.8018	Intermediate Similarity	NPC272898
0.8018	Intermediate Similarity	NPC473036
0.8	Intermediate Similarity	NPC277017
0.8	Intermediate Similarity	NPC475913
0.8	Intermediate Similarity	NPC84335
0.8	Intermediate Similarity	NPC118638
0.8	Intermediate Similarity	NPC154608
0.8	Intermediate Similarity	NPC19412
0.8	Intermediate Similarity	NPC474343
0.8	Intermediate Similarity	NPC38530
0.8	Intermediate Similarity	NPC473456
0.8	Intermediate Similarity	NPC192813
0.7982	Intermediate Similarity	NPC278628
0.7982	Intermediate Similarity	NPC266728
0.7982	Intermediate Similarity	NPC164600
0.7982	Intermediate Similarity	NPC103172
0.7982	Intermediate Similarity	NPC49492
0.7982	Intermediate Similarity	NPC231530
0.7981	Intermediate Similarity	NPC473170
0.7981	Intermediate Similarity	NPC98639
0.7981	Intermediate Similarity	NPC255809
0.7981	Intermediate Similarity	NPC139570
0.7981	Intermediate Similarity	NPC139459
0.7965	Intermediate Similarity	NPC202889
0.7963	Intermediate Similarity	NPC239716
0.7963	Intermediate Similarity	NPC471005
0.7963	Intermediate Similarity	NPC282233
0.7963	Intermediate Similarity	NPC159442
0.7963	Intermediate Similarity	NPC36321
0.7963	Intermediate Similarity	NPC236390
0.7963	Intermediate Similarity	NPC476237
0.7963	Intermediate Similarity	NPC33973
0.7963	Intermediate Similarity	NPC95585
0.7963	Intermediate Similarity	NPC70967
0.7963	Intermediate Similarity	NPC176883
0.7961	Intermediate Similarity	NPC477436
0.7961	Intermediate Similarity	NPC134826
0.7961	Intermediate Similarity	NPC474185
0.7961	Intermediate Similarity	NPC470375
0.7961	Intermediate Similarity	NPC470376
0.7961	Intermediate Similarity	NPC294263
0.7961	Intermediate Similarity	NPC477435
0.7949	Intermediate Similarity	NPC202051
0.7946	Intermediate Similarity	NPC231589
0.7946	Intermediate Similarity	NPC43775
0.7946	Intermediate Similarity	NPC201992
0.7946	Intermediate Similarity	NPC214797
0.7946	Intermediate Similarity	NPC118860
0.7944	Intermediate Similarity	NPC469327
0.7941	Intermediate Similarity	NPC126993
0.7941	Intermediate Similarity	NPC471896
0.7941	Intermediate Similarity	NPC85173
0.7934	Intermediate Similarity	NPC473593
0.7931	Intermediate Similarity	NPC474179
0.7931	Intermediate Similarity	NPC475834
0.7925	Intermediate Similarity	NPC252295
0.7925	Intermediate Similarity	NPC176845
0.7925	Intermediate Similarity	NPC477854
0.7925	Intermediate Similarity	NPC471717
0.7921	Intermediate Similarity	NPC328539
0.7917	Intermediate Similarity	NPC305496
0.7913	Intermediate Similarity	NPC476965
0.7913	Intermediate Similarity	NPC471854
0.7913	Intermediate Similarity	NPC470959
0.7909	Intermediate Similarity	NPC61071
0.7909	Intermediate Similarity	NPC473037
0.7909	Intermediate Similarity	NPC293512
0.7905	Intermediate Similarity	NPC328371
0.7905	Intermediate Similarity	NPC200054
0.7905	Intermediate Similarity	NPC29410
0.79	Intermediate Similarity	NPC6979
0.7895	Intermediate Similarity	NPC243354
0.7895	Intermediate Similarity	NPC474906
0.7895	Intermediate Similarity	NPC18547
0.789	Intermediate Similarity	NPC2436
0.789	Intermediate Similarity	NPC216245
0.789	Intermediate Similarity	NPC222161
0.789	Intermediate Similarity	NPC29705
0.789	Intermediate Similarity	NPC470251
0.789	Intermediate Similarity	NPC118911
0.789	Intermediate Similarity	NPC28656
0.789	Intermediate Similarity	NPC135854
0.7885	Intermediate Similarity	NPC240617
0.7885	Intermediate Similarity	NPC184870
0.7885	Intermediate Similarity	NPC471207
0.7876	Intermediate Similarity	NPC11252
0.7876	Intermediate Similarity	NPC100267
0.7876	Intermediate Similarity	NPC170487
0.7876	Intermediate Similarity	NPC475524
0.7876	Intermediate Similarity	NPC289312
0.7876	Intermediate Similarity	NPC205534

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 NPC469844 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	167
0.1-0.2	1486
0.2-0.3	3815
0.3-0.4	2462
0.4-0.5	714
0.5-0.6	201
0.6-0.7	154
0.7-0.8	117
0.8-0.85	34
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8364	Intermediate Similarity	NPD6882	Approved
0.8333	Intermediate Similarity	NPD6881	Approved
0.8333	Intermediate Similarity	NPD6899	Approved
0.8273	Intermediate Similarity	NPD6649	Approved
0.8273	Intermediate Similarity	NPD6650	Approved
0.8241	Intermediate Similarity	NPD5697	Approved
0.8218	Intermediate Similarity	NPD6079	Approved
0.8182	Intermediate Similarity	NPD7102	Approved
0.8182	Intermediate Similarity	NPD6883	Approved
0.8182	Intermediate Similarity	NPD7290	Approved
0.8165	Intermediate Similarity	NPD6011	Approved
0.8165	Intermediate Similarity	NPD7320	Approved
0.8148	Intermediate Similarity	NPD6675	Approved
0.8148	Intermediate Similarity	NPD7128	Approved
0.8148	Intermediate Similarity	NPD6402	Approved
0.8148	Intermediate Similarity	NPD5739	Approved
0.8137	Intermediate Similarity	NPD6399	Phase 3
0.8108	Intermediate Similarity	NPD6869	Approved
0.8108	Intermediate Similarity	NPD6847	Approved
0.8108	Intermediate Similarity	NPD8130	Phase 1
0.8108	Intermediate Similarity	NPD6617	Approved
0.8091	Intermediate Similarity	NPD6012	Approved
0.8091	Intermediate Similarity	NPD6014	Approved
0.8091	Intermediate Similarity	NPD6013	Approved
0.8091	Intermediate Similarity	NPD6372	Approved
0.8091	Intermediate Similarity	NPD6373	Approved
0.8036	Intermediate Similarity	NPD8297	Approved
0.8034	Intermediate Similarity	NPD6370	Approved
0.802	Intermediate Similarity	NPD5328	Approved
0.8	Intermediate Similarity	NPD7736	Approved
0.7982	Intermediate Similarity	NPD6008	Approved
0.7909	Intermediate Similarity	NPD5701	Approved
0.7905	Intermediate Similarity	NPD5220	Clinical (unspecified phase)
0.7905	Intermediate Similarity	NPD5222	Approved
0.7905	Intermediate Similarity	NPD5221	Approved
0.7899	Intermediate Similarity	NPD7492	Approved
0.7863	Intermediate Similarity	NPD6054	Approved
0.785	Intermediate Similarity	NPD4696	Approved
0.785	Intermediate Similarity	NPD5285	Approved
0.785	Intermediate Similarity	NPD5286	Approved
0.7833	Intermediate Similarity	NPD6616	Approved
0.783	Intermediate Similarity	NPD7902	Approved
0.783	Intermediate Similarity	NPD5173	Approved
0.7797	Intermediate Similarity	NPD6291	Clinical (unspecified phase)
0.7788	Intermediate Similarity	NPD6401	Clinical (unspecified phase)
0.7778	Intermediate Similarity	NPD5223	Approved
0.7769	Intermediate Similarity	NPD8293	Discontinued
0.7769	Intermediate Similarity	NPD7078	Approved
0.7759	Intermediate Similarity	NPD6009	Approved
0.7736	Intermediate Similarity	NPD4697	Phase 3
0.7723	Intermediate Similarity	NPD3618	Phase 1
0.7714	Intermediate Similarity	NPD7748	Approved
0.7706	Intermediate Similarity	NPD5226	Approved
0.7706	Intermediate Similarity	NPD5225	Approved
0.7706	Intermediate Similarity	NPD4633	Approved
0.7706	Intermediate Similarity	NPD5224	Approved
0.7706	Intermediate Similarity	NPD5211	Phase 2
0.7692	Intermediate Similarity	NPD6335	Approved
0.7692	Intermediate Similarity	NPD7515	Phase 2
0.7672	Intermediate Similarity	NPD6868	Approved
0.7664	Intermediate Similarity	NPD4755	Approved
0.7652	Intermediate Similarity	NPD4632	Approved
0.7647	Intermediate Similarity	NPD6015	Approved
0.7647	Intermediate Similarity	NPD6016	Approved
0.7642	Intermediate Similarity	NPD6356	Clinical (unspecified phase)
0.7636	Intermediate Similarity	NPD5174	Approved
0.7636	Intermediate Similarity	NPD5175	Approved
0.7627	Intermediate Similarity	NPD7100	Approved
0.7627	Intermediate Similarity	NPD7101	Approved
0.7607	Intermediate Similarity	NPD7115	Discovery
0.7607	Intermediate Similarity	NPD6317	Approved
0.7583	Intermediate Similarity	NPD5988	Approved
0.7568	Intermediate Similarity	NPD5141	Approved
0.7563	Intermediate Similarity	NPD6059	Approved
0.7547	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7547	Intermediate Similarity	NPD7900	Approved
0.7542	Intermediate Similarity	NPD6314	Approved
0.7542	Intermediate Similarity	NPD6313	Approved
0.7525	Intermediate Similarity	NPD4786	Approved
0.7523	Intermediate Similarity	NPD4700	Approved
0.7521	Intermediate Similarity	NPD6274	Approved
0.75	Intermediate Similarity	NPD6083	Phase 2
0.75	Intermediate Similarity	NPD6084	Phase 2
0.7476	Intermediate Similarity	NPD3573	Approved
0.7453	Intermediate Similarity	NPD4202	Approved
0.7434	Intermediate Similarity	NPD6412	Phase 2
0.7417	Intermediate Similarity	NPD6319	Approved
0.7404	Intermediate Similarity	NPD5737	Approved
0.7404	Intermediate Similarity	NPD6672	Approved
0.7404	Intermediate Similarity	NPD6903	Approved
0.7398	Intermediate Similarity	NPD7507	Approved
0.7379	Intermediate Similarity	NPD7146	Approved
0.7379	Intermediate Similarity	NPD6409	Approved
0.7379	Intermediate Similarity	NPD6684	Approved
0.7379	Intermediate Similarity	NPD7521	Approved
0.7379	Intermediate Similarity	NPD7334	Approved
0.7379	Intermediate Similarity	NPD5330	Approved
0.7377	Intermediate Similarity	NPD7604	Phase 2
0.7377	Intermediate Similarity	NPD8328	Phase 3
0.7368	Intermediate Similarity	NPD4730	Approved
0.7368	Intermediate Similarity	NPD4729	Approved
0.7358	Intermediate Similarity	NPD8035	Phase 2
0.7358	Intermediate Similarity	NPD8034	Phase 2
0.7355	Intermediate Similarity	NPD5983	Phase 2
0.7327	Intermediate Similarity	NPD3667	Approved
0.7321	Intermediate Similarity	NPD4754	Approved
0.7315	Intermediate Similarity	NPD1698	Clinical (unspecified phase)
0.7304	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.7282	Intermediate Similarity	NPD1694	Approved
0.7273	Intermediate Similarity	NPD7638	Approved
0.7273	Intermediate Similarity	NPD5696	Approved
0.7258	Intermediate Similarity	NPD6336	Discontinued
0.7241	Intermediate Similarity	NPD5169	Approved
0.7241	Intermediate Similarity	NPD5247	Approved
0.7241	Intermediate Similarity	NPD5251	Approved
0.7241	Intermediate Similarity	NPD5134	Clinical (unspecified phase)
0.7241	Intermediate Similarity	NPD4634	Approved
0.7241	Intermediate Similarity	NPD5135	Approved
0.7241	Intermediate Similarity	NPD5249	Phase 3
0.7241	Intermediate Similarity	NPD5250	Approved
0.7241	Intermediate Similarity	NPD5248	Approved
0.7238	Intermediate Similarity	NPD7513	Clinical (unspecified phase)
0.7236	Intermediate Similarity	NPD6067	Discontinued
0.7222	Intermediate Similarity	NPD7319	Approved
0.7222	Intermediate Similarity	NPD6001	Approved
0.7217	Intermediate Similarity	NPD5128	Approved
0.7217	Intermediate Similarity	NPD5168	Approved
0.7217	Intermediate Similarity	NPD6686	Approved
0.7213	Intermediate Similarity	NPD6908	Approved
0.7213	Intermediate Similarity	NPD6909	Approved
0.7212	Intermediate Similarity	NPD3574	Clinical (unspecified phase)
0.7207	Intermediate Similarity	NPD7640	Approved
0.7207	Intermediate Similarity	NPD7639	Approved
0.7196	Intermediate Similarity	NPD6411	Approved
0.7196	Intermediate Similarity	NPD5281	Approved
0.7196	Intermediate Similarity	NPD5284	Approved
0.7193	Intermediate Similarity	NPD4768	Approved
0.7193	Intermediate Similarity	NPD4767	Approved
0.7184	Intermediate Similarity	NPD3133	Approved
0.7184	Intermediate Similarity	NPD3666	Approved
0.7184	Intermediate Similarity	NPD3665	Phase 1
0.7179	Intermediate Similarity	NPD5215	Approved
0.7179	Intermediate Similarity	NPD5127	Approved
0.7179	Intermediate Similarity	NPD5217	Approved
0.7179	Intermediate Similarity	NPD5216	Approved
0.7167	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.7156	Intermediate Similarity	NPD5210	Approved
0.7156	Intermediate Similarity	NPD5695	Phase 3
0.7156	Intermediate Similarity	NPD4629	Approved
0.7143	Intermediate Similarity	NPD6033	Approved
0.7117	Intermediate Similarity	NPD4225	Approved
0.7115	Intermediate Similarity	NPD7520	Clinical (unspecified phase)
0.7103	Intermediate Similarity	NPD5207	Approved
0.7009	Intermediate Similarity	NPD4753	Phase 2
0.7009	Intermediate Similarity	NPD6080	Approved
0.7009	Intermediate Similarity	NPD5764	Clinical (unspecified phase)
0.7009	Intermediate Similarity	NPD6904	Approved
0.7009	Intermediate Similarity	NPD6101	Approved
0.7009	Intermediate Similarity	NPD6673	Approved
0.7	Intermediate Similarity	NPD5167	Approved
0.6887	Remote Similarity	NPD5279	Phase 3
0.6857	Remote Similarity	NPD3668	Phase 3
0.6852	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6833	Remote Similarity	NPD6053	Discontinued
0.6832	Remote Similarity	NPD6116	Phase 1
0.6829	Remote Similarity	NPD7328	Approved
0.6829	Remote Similarity	NPD7327	Approved
0.6827	Remote Similarity	NPD4223	Phase 3
0.6827	Remote Similarity	NPD4221	Approved
0.68	Remote Similarity	NPD8033	Approved
0.68	Remote Similarity	NPD7503	Approved
0.6796	Remote Similarity	NPD7525	Registered
0.6796	Remote Similarity	NPD4695	Discontinued
0.6792	Remote Similarity	NPD5329	Approved
0.6783	Remote Similarity	NPD7632	Discontinued
0.678	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD7516	Approved
0.6759	Remote Similarity	NPD5208	Approved
0.6733	Remote Similarity	NPD6117	Approved
0.6729	Remote Similarity	NPD5690	Phase 2
0.6729	Remote Similarity	NPD6098	Approved
0.6727	Remote Similarity	NPD6050	Approved
0.6727	Remote Similarity	NPD5693	Phase 1
0.6727	Remote Similarity	NPD5694	Approved
0.6724	Remote Similarity	NPD6052	Approved
0.6723	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.672	Remote Similarity	NPD8294	Approved
0.672	Remote Similarity	NPD8377	Approved
0.6698	Remote Similarity	NPD4197	Approved
0.6693	Remote Similarity	NPD7122	Discontinued
0.6667	Remote Similarity	NPD8380	Approved
0.6667	Remote Similarity	NPD8335	Approved
0.6667	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD8517	Approved
0.6667	Remote Similarity	NPD8513	Phase 3
0.6667	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD8379	Approved
0.6667	Remote Similarity	NPD6334	Approved
0.6667	Remote Similarity	NPD5779	Approved
0.6667	Remote Similarity	NPD8296	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