NPASS Compound

Structure

CID171550 OpenBabel06191715542D 26 30 0 0 1 0 0 0 0 0999 V2000 1.2321 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7248 2.9074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9328 3.8855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2601 1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4190 2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3090 0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4345 5.6215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2851 5.0035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4680 2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3090 0.9511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0981 4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8838 4.1945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 4.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6270 3.5254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5878 -0.8090 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 2.8412 4.7080 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2905 5.1081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4400 5.5170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4930 4.0254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 12 1 0 0 0 0 2 4 2 0 0 0 0 2 13 1 0 0 0 0 3 16 1 0 0 0 0 4 17 1 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 7 12 2 0 0 0 0 7 18 1 0 0 0 0 8 13 2 0 0 0 0 8 19 1 0 0 0 0 9 14 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 10 25 1 0 0 0 0 11 24 1 0 0 0 0 11 26 1 0 0 0 0 14 5 1 1 0 0 0 14 15 1 0 0 0 0 15 6 1 6 0 0 0 15 20 1 0 0 0 0 16 18 2 0 0 0 0 16 23 1 0 0 0 0 17 19 2 0 0 0 0 17 24 1 0 0 0 0 18 25 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	356.13
Volume:	348.616
LogP:	3.487
LogD:	2.954
LogS:	-5.303
# Rotatable Bonds:	4
TPSA:	66.38
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.908
Synthetic Accessibility Score:	3.541
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.908
MDCK Permeability:	3.343794378452003e-05
Pgp-inhibitor:	0.788
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.268
Plasma Protein Binding (PPB):	99.20796966552734%
Volume Distribution (VD):	0.673
Pgp-substrate:	2.0202102661132812%

ADMET: Metabolism

CYP1A2-inhibitor:	0.942
CYP1A2-substrate:	0.162
CYP2C19-inhibitor:	0.97
CYP2C19-substrate:	0.228
CYP2C9-inhibitor:	0.691
CYP2C9-substrate:	0.636
CYP2D6-inhibitor:	0.991
CYP2D6-substrate:	0.917
CYP3A4-inhibitor:	0.975
CYP3A4-substrate:	0.651

ADMET: Excretion

Clearance (CL):	16.252
Half-life (T1/2):	0.297

ADMET: Toxicity

hERG Blockers:	0.342
Human Hepatotoxicity (H-HT):	0.265
Drug-inuced Liver Injury (DILI):	0.851
AMES Toxicity:	0.066
Rat Oral Acute Toxicity:	0.014
Maximum Recommended Daily Dose:	0.535
Skin Sensitization:	0.78
Carcinogencity:	0.891
Eye Corrosion:	0.003
Eye Irritation:	0.056
Respiratory Toxicity:	0.484

Download Data

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

Natural Product: NPC171550

Natural Product ID:	NPC171550
*Common Name:**	Cubebin
IUPAC Name:	(3R,4R)-3,4-bis(1,3-benzodioxol-5-ylmethyl)oxolan-2-ol
Synonyms:
Standard InCHIKey:	DIYWRNLYKJKHAM-VKWYCSODSA-N
Standard InCHI:	InChI=1S/C20H20O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15,20-21H,5-6,9-11H2/t14-,15+,20?/m0/s1
SMILES:	OC1OC[C@@H]([C@H]1Cc1ccc2c(c1)OCO2)Cc1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3752996
PubChem CID:	14137603
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001968] Dibenzylbutyrolactols

*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
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679319]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[18177011]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19271742]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590154]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	roots	n.a.	n.a.	PMID[26259802]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8064299]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Resin, Exudate, Sap	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20173	Aristolochia triangularis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20173	Aristolochia triangularis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11169	Piper cubeba	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20173	Aristolochia triangularis	Species	Aristolochiaceae	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
NON-MOLECULAR	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	15700.0	nM	PMID[548335]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	38200.0	nM	PMID[548335]

☑ 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 NPC171550 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	366
0.1-0.2	1384
0.2-0.3	3588
0.3-0.4	10976
0.4-0.5	8325
0.5-0.6	7889
0.6-0.7	7366
0.7-0.8	2321
0.8-0.85	331
0.85-0.9	126
0.9-0.95	20
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC134764
0.9675	High Similarity	NPC213711
0.9675	High Similarity	NPC40352
0.9597	High Similarity	NPC158737
0.9531	High Similarity	NPC47181
0.9462	High Similarity	NPC469981
0.9457	High Similarity	NPC18576
0.9453	High Similarity	NPC169973
0.9248	High Similarity	NPC471908
0.9225	High Similarity	NPC147616
0.9225	High Similarity	NPC219671
0.9225	High Similarity	NPC259742
0.9225	High Similarity	NPC104077
0.9219	High Similarity	NPC173308
0.9219	High Similarity	NPC271208
0.9219	High Similarity	NPC233224
0.9219	High Similarity	NPC181079
0.9219	High Similarity	NPC275950
0.9173	High Similarity	NPC56091
0.9167	High Similarity	NPC185908
0.9167	High Similarity	NPC101807
0.9147	High Similarity	NPC476345
0.9147	High Similarity	NPC82111
0.9147	High Similarity	NPC227160
0.9113	High Similarity	NPC301641
0.9113	High Similarity	NPC80241
0.9098	High Similarity	NPC193666
0.9098	High Similarity	NPC123526
0.9098	High Similarity	NPC88640
0.9098	High Similarity	NPC156376
0.9077	High Similarity	NPC129687
0.9077	High Similarity	NPC158526
0.9077	High Similarity	NPC171928
0.9077	High Similarity	NPC33611
0.9077	High Similarity	NPC16830
0.9077	High Similarity	NPC100223
0.9062	High Similarity	NPC165128
0.9062	High Similarity	NPC226862
0.9062	High Similarity	NPC57119
0.9062	High Similarity	NPC158471
0.903	High Similarity	NPC46591
0.9023	High Similarity	NPC283949
0.9015	High Similarity	NPC135777
0.9015	High Similarity	NPC142547
0.9015	High Similarity	NPC101624
0.9015	High Similarity	NPC184938
0.8992	High Similarity	NPC476748
0.8968	High Similarity	NPC249788
0.8952	High Similarity	NPC344161
0.8931	High Similarity	NPC106739
0.8906	High Similarity	NPC274356
0.8905	High Similarity	NPC179521
0.8897	High Similarity	NPC246947
0.8889	High Similarity	NPC226547
0.8872	High Similarity	NPC474139
0.8872	High Similarity	NPC174191
0.8872	High Similarity	NPC150534
0.8872	High Similarity	NPC189474
0.8864	High Similarity	NPC196937
0.8841	High Similarity	NPC469586
0.8832	High Similarity	NPC265154
0.8832	High Similarity	NPC477898
0.8832	High Similarity	NPC298317
0.8832	High Similarity	NPC255566
0.8797	High Similarity	NPC110958
0.8797	High Similarity	NPC19890
0.8797	High Similarity	NPC31530
0.879	High Similarity	NPC474040
0.8788	High Similarity	NPC7744
0.8788	High Similarity	NPC471505
0.8777	High Similarity	NPC3982
0.8768	High Similarity	NPC141569
0.8768	High Similarity	NPC84181
0.8768	High Similarity	NPC477701
0.8768	High Similarity	NPC166884
0.876	High Similarity	NPC206882
0.8759	High Similarity	NPC302506
0.8731	High Similarity	NPC25333
0.8731	High Similarity	NPC49235
0.8731	High Similarity	NPC236522
0.8731	High Similarity	NPC148893
0.8722	High Similarity	NPC136750
0.8722	High Similarity	NPC266848
0.8712	High Similarity	NPC192255
0.8705	High Similarity	NPC38041
0.8705	High Similarity	NPC279298
0.8705	High Similarity	NPC22150
0.8696	High Similarity	NPC185071
0.8696	High Similarity	NPC12728
0.8692	High Similarity	NPC177167
0.8686	High Similarity	NPC472711
0.8672	High Similarity	NPC317769
0.8672	High Similarity	NPC31344
0.8657	High Similarity	NPC170779
0.8657	High Similarity	NPC90083
0.8647	High Similarity	NPC261812
0.8647	High Similarity	NPC65183
0.8647	High Similarity	NPC97316
0.8647	High Similarity	NPC72046
0.8643	High Similarity	NPC276753
0.8643	High Similarity	NPC205796
0.8643	High Similarity	NPC112861
0.8626	High Similarity	NPC470084
0.8623	High Similarity	NPC287124
0.8623	High Similarity	NPC311057
0.8613	High Similarity	NPC177868
0.8605	High Similarity	NPC121783
0.8605	High Similarity	NPC34902
0.8605	High Similarity	NPC18449
0.8594	High Similarity	NPC85488
0.8582	High Similarity	NPC205915
0.8571	High Similarity	NPC18979
0.8571	High Similarity	NPC158079
0.8571	High Similarity	NPC228346
0.8571	High Similarity	NPC7171
0.8571	High Similarity	NPC161557
0.8571	High Similarity	NPC27843
0.8571	High Similarity	NPC115207
0.8571	High Similarity	NPC40432
0.8561	High Similarity	NPC470950
0.8561	High Similarity	NPC475875
0.8561	High Similarity	NPC474808
0.8561	High Similarity	NPC185307
0.8551	High Similarity	NPC282291
0.8551	High Similarity	NPC166137
0.8551	High Similarity	NPC312199
0.854	High Similarity	NPC113550
0.8538	High Similarity	NPC17348
0.8529	High Similarity	NPC230968
0.8529	High Similarity	NPC102260
0.8527	High Similarity	NPC280704
0.8519	High Similarity	NPC476411
0.8516	High Similarity	NPC65933
0.8516	High Similarity	NPC172676
0.8516	High Similarity	NPC126935
0.8516	High Similarity	NPC312713
0.8516	High Similarity	NPC57268
0.8516	High Similarity	NPC216929
0.8511	High Similarity	NPC241846
0.8511	High Similarity	NPC93610
0.8507	High Similarity	NPC207400
0.8507	High Similarity	NPC181049
0.8507	High Similarity	NPC227002
0.85	High Similarity	NPC129417
0.85	High Similarity	NPC471063
0.85	High Similarity	NPC79429
0.85	High Similarity	NPC217635
0.85	High Similarity	NPC471667
0.85	High Similarity	NPC473575
0.85	High Similarity	NPC283995
0.85	High Similarity	NPC470235
0.8496	Intermediate Similarity	NPC153739
0.8496	Intermediate Similarity	NPC242807
0.8496	Intermediate Similarity	NPC64201
0.8496	Intermediate Similarity	NPC92164
0.8496	Intermediate Similarity	NPC241522
0.8496	Intermediate Similarity	NPC145305
0.8496	Intermediate Similarity	NPC42300
0.8496	Intermediate Similarity	NPC77040
0.8496	Intermediate Similarity	NPC174495
0.8496	Intermediate Similarity	NPC187998
0.8496	Intermediate Similarity	NPC257582
0.8492	Intermediate Similarity	NPC474214
0.8489	Intermediate Similarity	NPC253878
0.8489	Intermediate Similarity	NPC476356
0.8485	Intermediate Similarity	NPC282703
0.8485	Intermediate Similarity	NPC184733
0.8485	Intermediate Similarity	NPC21867
0.8485	Intermediate Similarity	NPC11258
0.8485	Intermediate Similarity	NPC128208
0.8485	Intermediate Similarity	NPC45774
0.8485	Intermediate Similarity	NPC129570
0.848	Intermediate Similarity	NPC81067
0.848	Intermediate Similarity	NPC9341
0.8467	Intermediate Similarity	NPC474039
0.8462	Intermediate Similarity	NPC51328
0.8462	Intermediate Similarity	NPC286235
0.8462	Intermediate Similarity	NPC240521
0.8462	Intermediate Similarity	NPC55158
0.8444	Intermediate Similarity	NPC112237
0.844	Intermediate Similarity	NPC180953
0.844	Intermediate Similarity	NPC43508
0.844	Intermediate Similarity	NPC476301
0.8433	Intermediate Similarity	NPC277804
0.8429	Intermediate Similarity	NPC46092
0.8425	Intermediate Similarity	NPC474320
0.8421	Intermediate Similarity	NPC26653
0.8421	Intermediate Similarity	NPC270849
0.8417	Intermediate Similarity	NPC246474
0.8417	Intermediate Similarity	NPC471414
0.8417	Intermediate Similarity	NPC218092
0.8417	Intermediate Similarity	NPC162851
0.8406	Intermediate Similarity	NPC9068
0.8403	Intermediate Similarity	NPC475224
0.8403	Intermediate Similarity	NPC238140
0.8403	Intermediate Similarity	NPC98624
0.8394	Intermediate Similarity	NPC121651
0.8394	Intermediate Similarity	NPC25695
0.8394	Intermediate Similarity	NPC52277
0.8394	Intermediate Similarity	NPC172818

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 NPC171550 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	290
0.1-0.2	847
0.2-0.3	1623
0.3-0.4	2783
0.4-0.5	1876
0.5-0.6	1138
0.6-0.7	520
0.7-0.8	70
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
0.8387	Intermediate Similarity	NPD5283	Phase 1
0.8372	Intermediate Similarity	NPD3705	Approved
0.8281	Intermediate Similarity	NPD1357	Approved
0.7883	Intermediate Similarity	NPD3027	Phase 3
0.7829	Intermediate Similarity	NPD4966	Approved
0.7829	Intermediate Similarity	NPD4967	Phase 2
0.7829	Intermediate Similarity	NPD4965	Approved
0.7808	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7778	Intermediate Similarity	NPD6674	Discontinued
0.7671	Intermediate Similarity	NPD5084	Clinical (unspecified phase)
0.7656	Intermediate Similarity	NPD228	Approved
0.7632	Intermediate Similarity	NPD37	Approved
0.7613	Intermediate Similarity	NPD6234	Discontinued
0.7589	Intermediate Similarity	NPD3620	Phase 2
0.7589	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.7559	Intermediate Similarity	NPD2684	Approved
0.7557	Intermediate Similarity	NPD7157	Approved
0.7516	Intermediate Similarity	NPD7199	Phase 2
0.75	Intermediate Similarity	NPD4108	Discontinued
0.75	Intermediate Similarity	NPD3021	Approved
0.75	Intermediate Similarity	NPD7228	Approved
0.75	Intermediate Similarity	NPD7028	Phase 2
0.75	Intermediate Similarity	NPD3022	Approved
0.7483	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7483	Intermediate Similarity	NPD4110	Phase 3
0.7482	Intermediate Similarity	NPD2861	Phase 2
0.7468	Intermediate Similarity	NPD5563	Clinical (unspecified phase)
0.7465	Intermediate Similarity	NPD1613	Approved
0.7465	Intermediate Similarity	NPD4060	Phase 1
0.7465	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7462	Intermediate Similarity	NPD7843	Approved
0.7445	Intermediate Similarity	NPD4379	Clinical (unspecified phase)
0.7444	Intermediate Similarity	NPD5536	Phase 2
0.7426	Intermediate Similarity	NPD1091	Approved
0.7397	Intermediate Similarity	NPD1375	Discontinued
0.7397	Intermediate Similarity	NPD7266	Discontinued
0.7383	Intermediate Similarity	NPD6783	Clinical (unspecified phase)
0.7365	Intermediate Similarity	NPD6331	Phase 2
0.7355	Intermediate Similarity	NPD2978	Approved
0.7355	Intermediate Similarity	NPD2977	Approved
0.7329	Intermediate Similarity	NPD2161	Phase 2
0.7324	Intermediate Similarity	NPD5110	Phase 2
0.7324	Intermediate Similarity	NPD5111	Phase 2
0.7324	Intermediate Similarity	NPD5109	Approved
0.7319	Intermediate Similarity	NPD3600	Clinical (unspecified phase)
0.7317	Intermediate Similarity	NPD7240	Approved
0.7312	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7305	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7297	Intermediate Similarity	NPD4236	Phase 3
0.7297	Intermediate Similarity	NPD4237	Approved
0.7292	Intermediate Similarity	NPD6355	Discontinued
0.7292	Intermediate Similarity	NPD5735	Approved
0.7279	Intermediate Similarity	NPD6516	Phase 2
0.7279	Intermediate Similarity	NPD5846	Approved
0.7267	Intermediate Similarity	NPD5058	Phase 3
0.7254	Intermediate Similarity	NPD7095	Approved
0.7234	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD4140	Approved
0.7194	Intermediate Similarity	NPD2982	Phase 2
0.7194	Intermediate Similarity	NPD2983	Phase 2
0.7194	Intermediate Similarity	NPD3685	Discontinued
0.7183	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7178	Intermediate Similarity	NPD3818	Discontinued
0.7172	Intermediate Similarity	NPD3657	Discovery
0.7153	Intermediate Similarity	NPD1726	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD6028	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD6029	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD5588	Approved
0.7143	Intermediate Similarity	NPD1653	Approved
0.7132	Intermediate Similarity	NPD1182	Approved
0.7132	Intermediate Similarity	NPD968	Approved
0.7122	Intermediate Similarity	NPD2981	Phase 2
0.7122	Intermediate Similarity	NPD2231	Phase 2
0.7122	Intermediate Similarity	NPD1840	Phase 2
0.7122	Intermediate Similarity	NPD2235	Phase 2
0.7113	Intermediate Similarity	NPD3018	Phase 2
0.708	Intermediate Similarity	NPD5585	Approved
0.7078	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7075	Intermediate Similarity	NPD6896	Approved
0.7075	Intermediate Similarity	NPD6895	Approved
0.7075	Intermediate Similarity	NPD7097	Phase 1
0.7071	Intermediate Similarity	NPD5327	Phase 3
0.7068	Intermediate Similarity	NPD5535	Approved
0.7067	Intermediate Similarity	NPD5177	Phase 3
0.7067	Intermediate Similarity	NPD4162	Approved
0.7067	Intermediate Similarity	NPD3060	Approved
0.7063	Intermediate Similarity	NPD4908	Phase 1
0.7063	Intermediate Similarity	NPD3020	Approved
0.705	Intermediate Similarity	NPD1610	Phase 2
0.7047	Intermediate Similarity	NPD5762	Approved
0.7047	Intermediate Similarity	NPD5763	Approved
0.7042	Intermediate Similarity	NPD6584	Phase 3
0.7042	Intermediate Similarity	NPD4624	Approved
0.7037	Intermediate Similarity	NPD709	Approved
0.7037	Intermediate Similarity	NPD6671	Approved
0.7034	Intermediate Similarity	NPD554	Clinical (unspecified phase)
0.7029	Intermediate Similarity	NPD5126	Approved
0.7029	Intermediate Similarity	NPD2668	Approved
0.7029	Intermediate Similarity	NPD2667	Approved
0.7029	Intermediate Similarity	NPD5125	Phase 3
0.7021	Intermediate Similarity	NPD1283	Approved
0.7013	Intermediate Similarity	NPD52	Approved
0.7013	Intermediate Similarity	NPD7527	Clinical (unspecified phase)
0.7013	Intermediate Similarity	NPD7526	Approved
0.7007	Intermediate Similarity	NPD2492	Phase 1
0.7007	Intermediate Similarity	NPD6653	Approved
0.7007	Intermediate Similarity	NPD6353	Approved
0.7	Intermediate Similarity	NPD2230	Approved
0.7	Intermediate Similarity	NPD2233	Approved
0.7	Intermediate Similarity	NPD2232	Approved
0.7	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.6986	Remote Similarity	NPD2979	Phase 3
0.6978	Remote Similarity	NPD3847	Discontinued
0.6974	Remote Similarity	NPD5241	Discontinued
0.6974	Remote Similarity	NPD5307	Clinical (unspecified phase)
0.697	Remote Similarity	NPD5451	Approved
0.6966	Remote Similarity	NPD4907	Clinical (unspecified phase)
0.6966	Remote Similarity	NPD6798	Discontinued
0.6962	Remote Similarity	NPD7945	Clinical (unspecified phase)
0.6959	Remote Similarity	NPD4536	Approved
0.6959	Remote Similarity	NPD4537	Clinical (unspecified phase)
0.6959	Remote Similarity	NPD4538	Approved
0.6957	Remote Similarity	NPD5691	Approved
0.6954	Remote Similarity	NPD5698	Clinical (unspecified phase)
0.6947	Remote Similarity	NPD1358	Approved
0.6947	Remote Similarity	NPD290	Approved
0.694	Remote Similarity	NPD1138	Approved
0.6918	Remote Similarity	NPD8455	Phase 2
0.6918	Remote Similarity	NPD6233	Phase 2
0.6913	Remote Similarity	NPD5960	Phase 3
0.6912	Remote Similarity	NPD6387	Discontinued
0.6908	Remote Similarity	NPD6658	Clinical (unspecified phase)
0.6906	Remote Similarity	NPD4626	Approved
0.6905	Remote Similarity	NPD7685	Pre-registration
0.6903	Remote Similarity	NPD5261	Clinical (unspecified phase)
0.6901	Remote Similarity	NPD8651	Approved
0.6901	Remote Similarity	NPD2922	Phase 1
0.6894	Remote Similarity	NPD5604	Discontinued
0.6892	Remote Similarity	NPD2157	Approved
0.6887	Remote Similarity	NPD7037	Approved
0.6887	Remote Similarity	NPD5958	Discontinued
0.6886	Remote Similarity	NPD7074	Phase 3
0.6884	Remote Similarity	NPD1894	Discontinued
0.6882	Remote Similarity	NPD7090	Clinical (unspecified phase)
0.6879	Remote Similarity	NPD1608	Approved
0.6871	Remote Similarity	NPD8127	Discontinued
0.6871	Remote Similarity	NPD5837	Clinical (unspecified phase)
0.6871	Remote Similarity	NPD2238	Phase 2
0.6871	Remote Similarity	NPD1558	Phase 1
0.687	Remote Similarity	NPD3134	Approved
0.6867	Remote Similarity	NPD6032	Approved
0.6867	Remote Similarity	NPD2438	Suspended
0.6866	Remote Similarity	NPD1139	Approved
0.6866	Remote Similarity	NPD1137	Approved
0.686	Remote Similarity	NPD7243	Clinical (unspecified phase)
0.6857	Remote Similarity	NPD3496	Discontinued
0.6849	Remote Similarity	NPD5718	Phase 2
0.6846	Remote Similarity	NPD7119	Phase 2
0.6842	Remote Similarity	NPD8055	Clinical (unspecified phase)
0.6839	Remote Similarity	NPD4123	Phase 3
0.6839	Remote Similarity	NPD4739	Approved
0.6835	Remote Similarity	NPD1651	Approved
0.6833	Remote Similarity	NPD7680	Approved
0.6831	Remote Similarity	NPD4359	Approved
0.6831	Remote Similarity	NPD6582	Phase 2
0.6831	Remote Similarity	NPD1669	Approved
0.6831	Remote Similarity	NPD6583	Phase 3
0.6826	Remote Similarity	NPD7054	Approved
0.6825	Remote Similarity	NPD2859	Approved
0.6825	Remote Similarity	NPD2860	Approved
0.6824	Remote Similarity	NPD7280	Phase 3
0.6824	Remote Similarity	NPD7281	Phase 3
0.6822	Remote Similarity	NPD291	Approved
0.6815	Remote Similarity	NPD821	Approved
0.6815	Remote Similarity	NPD4210	Discontinued
0.6809	Remote Similarity	NPD1281	Approved
0.6806	Remote Similarity	NPD558	Phase 2
0.6803	Remote Similarity	NPD2674	Phase 3
0.6803	Remote Similarity	NPD4062	Phase 3
0.6797	Remote Similarity	NPD4628	Phase 3
0.6786	Remote Similarity	NPD3095	Discontinued
0.6786	Remote Similarity	NPD7472	Approved
0.6776	Remote Similarity	NPD4664	Clinical (unspecified phase)
0.6772	Remote Similarity	NPD7458	Discontinued
0.6772	Remote Similarity	NPD4005	Discontinued
0.677	Remote Similarity	NPD6374	Clinical (unspecified phase)
0.6763	Remote Similarity	NPD3091	Approved
0.6763	Remote Similarity	NPD1548	Phase 1
0.6759	Remote Similarity	NPD1712	Approved
0.6753	Remote Similarity	NPD2677	Approved
0.675	Remote Similarity	NPD3382	Approved
0.675	Remote Similarity	NPD3383	Approved
0.675	Remote Similarity	NPD3384	Approved
0.6746	Remote Similarity	NPD2934	Approved
0.6746	Remote Similarity	NPD2933	Approved
0.6741	Remote Similarity	NPD969	Suspended
0.6739	Remote Similarity	NPD3596	Phase 2
0.6736	Remote Similarity	NPD3094	Phase 2
0.6735	Remote Similarity	NPD3144	Approved
0.6735	Remote Similarity	NPD3145	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