NPASS Compound

Structure

CID232258 OpenBabel06191716032D 43 48 0 0 1 0 0 0 0 0999 V2000 1.0286 3.1688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5178 3.5544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7926 2.3037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4985 -1.6679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6460 -1.1760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0893 1.2832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0896 0.2996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4977 1.2842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6452 1.7761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2027 -1.6674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3845 2.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0541 -0.1908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8511 -1.4751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8289 1.3726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0065 3.0663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9401 2.7588 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.3508 -1.1755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4066 2.1682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0544 -1.1750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.6457 -0.1918 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.4980 0.3006 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9404 1.7756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7932 0.3001 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.2022 0.3011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9622 2.8613 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8514 -0.4919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.3505 -0.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7030 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7033 0.9827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8519 1.4746 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5842 3.8619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9832 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7929 1.2837 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0006 -1.9664 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.9206 -1.6748 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2019 1.3011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5544 -0.4923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5549 1.4741 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8522 2.4578 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1840 4.7600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8511 1.4751 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5620 3.7594 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 15 1 0 0 0 0 4 5 1 0 0 0 0 4 17 1 0 0 0 0 6 7 1 0 0 0 0 6 22 1 0 0 0 0 7 23 1 0 0 0 0 8 9 1 0 0 0 0 9 33 1 0 0 0 0 10 17 1 0 0 0 0 10 19 1 0 0 0 0 11 18 1 0 0 0 0 11 25 1 0 0 0 0 12 19 1 0 0 0 0 12 24 1 0 0 0 0 13 34 1 0 0 0 0 14 18 1 0 0 0 0 14 41 1 0 0 0 0 15 18 2 0 0 0 0 15 31 1 0 0 0 0 16 2 1 1 0 0 0 16 22 1 0 0 0 0 17 27 2 0 0 0 0 19 35 1 6 0 0 0 20 5 1 1 0 0 0 20 21 1 0 0 0 0 20 23 1 0 0 0 0 21 8 1 6 0 0 0 21 27 1 0 0 0 0 22 33 1 6 0 0 0 23 33 1 6 0 0 0 24 27 1 0 0 0 0 24 36 2 0 0 0 0 25 16 1 1 0 0 0 25 42 1 0 0 0 0 26 13 1 6 0 0 0 26 28 1 0 0 0 0 26 43 1 0 0 0 0 28 29 1 0 0 0 0 28 37 1 1 0 0 0 29 30 1 0 0 0 0 29 38 1 6 0 0 0 30 32 1 0 0 0 0 30 39 1 1 0 0 0 31 40 2 0 0 0 0 31 42 1 0 0 0 0 32 41 1 6 0 0 0 32 43 1 0 0 0 0 33 3 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	604.32
Volume:	605.342
LogP:	2.428
LogD:	2.522
LogS:	-3.619
# Rotatable Bonds:	6
TPSA:	162.98
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.223
Synthetic Accessibility Score:	5.605
Fsp3:	0.818
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.763
MDCK Permeability:	4.5960019633639604e-05
Pgp-inhibitor:	0.27
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.945
20% Bioavailability (F20%):	0.386
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.027
Plasma Protein Binding (PPB):	76.66178131103516%
Volume Distribution (VD):	0.836
Pgp-substrate:	6.638199806213379%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.096
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.306
CYP2C9-inhibitor:	0.036
CYP2C9-substrate:	0.046
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.045
CYP3A4-inhibitor:	0.435
CYP3A4-substrate:	0.295

ADMET: Excretion

Clearance (CL):	2.323
Half-life (T1/2):	0.769

ADMET: Toxicity

hERG Blockers:	0.048
Human Hepatotoxicity (H-HT):	0.198
Drug-inuced Liver Injury (DILI):	0.394
AMES Toxicity:	0.077
Rat Oral Acute Toxicity:	0.637
Maximum Recommended Daily Dose:	0.922
Skin Sensitization:	0.046
Carcinogencity:	0.838
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.266

Download Data

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

Natural Product: NPC232258

Natural Product ID:	NPC232258
*Common Name:**	Withalongolide M
IUPAC Name:	(2R)-2-[(1S)-1-[(3R,8S,9S,13S,14S,17R)-3-hydroxy-13-methyl-1-oxo-3,4,6,7,8,9,11,12,14,15,16,17-dodecahydro-2H-cyclopenta[a]phenanthren-17-yl]ethyl]-5-methyl-4-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]-2,3-dihydropyran-6-one
Synonyms:	Withalongolide M
Standard InCHIKey:	CLUVBNATYXEVRS-UJQMTUMNSA-N
Standard InCHI:	InChI=1S/C33H48O10/c1-15-18(14-41-32-30(39)29(38)28(37)26(13-34)43-32)11-25(42-31(15)40)16(2)22-6-7-23-20-5-4-17-10-19(35)12-24(36)27(17)21(20)8-9-33(22,23)3/h16,19-23,25-26,28-30,32,34-35,37-39H,4-14H2,1-3H3/t16-,19+,20+,21-,22+,23-,25+,26+,28+,29-,30+,32+,33+/m0/s1
SMILES:	CC1=C(C[C@H]([C@@H](C)[C@H]2CC[C@H]3[C@@H]4CCC5=C([C@H]4CC[C@]23C)C(=O)C[C@@H](C5)O)OC1=O)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1934465
PubChem CID:	56926294
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

*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
NPO14874	Physalis longifolia	Species	Solanaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[22098611]
NPO14874	Physalis longifolia	Species	Solanaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[22098611]
NPO14874	Physalis longifolia	Species	Solanaceae	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	5

Activity Type	# Activity
Cell Line	2
NON-MOLECULAR	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT169	Cell Line	B16-F10	Mus musculus	IC50	>	10000.0	nM	PMID[459561]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	IC50	>	10000.0	nM	PMID[459561]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[459561]
NPT27	Others	Unspecified		IC50	>	10000.0	nM	PMID[459561]

☑ 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 NPC232258 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	269
0.1-0.2	1582
0.2-0.3	4911
0.3-0.4	9161
0.4-0.5	11094
0.5-0.6	6976
0.6-0.7	5821
0.7-0.8	2738
0.8-0.85	116
0.85-0.9	24
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.982	High Similarity	NPC129434
0.9727	High Similarity	NPC291564
0.9316	High Similarity	NPC245094
0.9224	High Similarity	NPC318135
0.9076	High Similarity	NPC476966
0.9	High Similarity	NPC173347
0.8966	High Similarity	NPC170084
0.8966	High Similarity	NPC476204
0.8926	High Similarity	NPC231240
0.8852	High Similarity	NPC316915
0.8839	High Similarity	NPC477073
0.8829	High Similarity	NPC477070
0.8829	High Similarity	NPC477069
0.8803	High Similarity	NPC202051
0.8761	High Similarity	NPC477253
0.8761	High Similarity	NPC233003
0.8696	High Similarity	NPC207637
0.8684	High Similarity	NPC477074
0.8684	High Similarity	NPC251309
0.8678	High Similarity	NPC311534
0.8644	High Similarity	NPC278163
0.8644	High Similarity	NPC187950
0.8632	High Similarity	NPC477071
0.8621	High Similarity	NPC477252
0.8584	High Similarity	NPC129340
0.8571	High Similarity	NPC195708
0.8559	High Similarity	NPC476127
0.8559	High Similarity	NPC476150
0.8559	High Similarity	NPC470312
0.8547	High Similarity	NPC473617
0.8547	High Similarity	NPC473828
0.8547	High Similarity	NPC239293
0.8496	Intermediate Similarity	NPC265655
0.8468	Intermediate Similarity	NPC223741
0.8462	Intermediate Similarity	NPC474483
0.8455	Intermediate Similarity	NPC471407
0.8455	Intermediate Similarity	NPC473593
0.8448	Intermediate Similarity	NPC116024
0.8448	Intermediate Similarity	NPC473882
0.8448	Intermediate Similarity	NPC220293
0.8443	Intermediate Similarity	NPC42399
0.843	Intermediate Similarity	NPC7850
0.843	Intermediate Similarity	NPC6615
0.8421	Intermediate Similarity	NPC114961
0.8421	Intermediate Similarity	NPC475243
0.8421	Intermediate Similarity	NPC27551
0.8421	Intermediate Similarity	NPC90630
0.8407	Intermediate Similarity	NPC295389
0.8393	Intermediate Similarity	NPC162033
0.8362	Intermediate Similarity	NPC260665
0.8361	Intermediate Similarity	NPC47113
0.8361	Intermediate Similarity	NPC174367
0.8348	Intermediate Similarity	NPC285410
0.8348	Intermediate Similarity	NPC292196
0.8348	Intermediate Similarity	NPC263827
0.8348	Intermediate Similarity	NPC250481
0.8333	Intermediate Similarity	NPC412
0.8333	Intermediate Similarity	NPC246205
0.8333	Intermediate Similarity	NPC258789
0.8333	Intermediate Similarity	NPC194310
0.8333	Intermediate Similarity	NPC118225
0.8333	Intermediate Similarity	NPC258815
0.8333	Intermediate Similarity	NPC241310
0.8333	Intermediate Similarity	NPC131841
0.8333	Intermediate Similarity	NPC169727
0.8333	Intermediate Similarity	NPC475182
0.8333	Intermediate Similarity	NPC47567
0.8333	Intermediate Similarity	NPC475364
0.8333	Intermediate Similarity	NPC31522
0.832	Intermediate Similarity	NPC471855
0.8319	Intermediate Similarity	NPC258592
0.8319	Intermediate Similarity	NPC178548
0.8319	Intermediate Similarity	NPC474179
0.8319	Intermediate Similarity	NPC475834
0.8293	Intermediate Similarity	NPC329784
0.8293	Intermediate Similarity	NPC471357
0.8293	Intermediate Similarity	NPC146456
0.8293	Intermediate Similarity	NPC469757
0.8293	Intermediate Similarity	NPC117702
0.8293	Intermediate Similarity	NPC470516
0.8293	Intermediate Similarity	NPC240070
0.8291	Intermediate Similarity	NPC475163
0.8291	Intermediate Similarity	NPC74727
0.8291	Intermediate Similarity	NPC165439
0.8279	Intermediate Similarity	NPC177820
0.8279	Intermediate Similarity	NPC30188
0.8279	Intermediate Similarity	NPC248202
0.8279	Intermediate Similarity	NPC130229
0.8279	Intermediate Similarity	NPC3381
0.8276	Intermediate Similarity	NPC474265
0.8276	Intermediate Similarity	NPC210420
0.8276	Intermediate Similarity	NPC471967
0.8264	Intermediate Similarity	NPC23786
0.8264	Intermediate Similarity	NPC156789
0.8264	Intermediate Similarity	NPC470265
0.8261	Intermediate Similarity	NPC154856
0.8261	Intermediate Similarity	NPC83005
0.8261	Intermediate Similarity	NPC52241
0.8261	Intermediate Similarity	NPC475317
0.8254	Intermediate Similarity	NPC469749
0.8254	Intermediate Similarity	NPC32793
0.8254	Intermediate Similarity	NPC116075
0.8254	Intermediate Similarity	NPC247190
0.8254	Intermediate Similarity	NPC146857
0.825	Intermediate Similarity	NPC129393
0.825	Intermediate Similarity	NPC476849
0.825	Intermediate Similarity	NPC251226
0.825	Intermediate Similarity	NPC281840
0.8246	Intermediate Similarity	NPC300614
0.8246	Intermediate Similarity	NPC90946
0.8246	Intermediate Similarity	NPC285576
0.824	Intermediate Similarity	NPC213634
0.8235	Intermediate Similarity	NPC45475
0.8235	Intermediate Similarity	NPC86020
0.8235	Intermediate Similarity	NPC475632
0.8235	Intermediate Similarity	NPC475913
0.8226	Intermediate Similarity	NPC473620
0.8205	Intermediate Similarity	NPC200944
0.8205	Intermediate Similarity	NPC75167
0.8205	Intermediate Similarity	NPC311592
0.8205	Intermediate Similarity	NPC73986
0.8205	Intermediate Similarity	NPC73455
0.8197	Intermediate Similarity	NPC41129
0.8197	Intermediate Similarity	NPC27363
0.8197	Intermediate Similarity	NPC160084
0.819	Intermediate Similarity	NPC31839
0.819	Intermediate Similarity	NPC11035
0.819	Intermediate Similarity	NPC190837
0.8189	Intermediate Similarity	NPC329636
0.8182	Intermediate Similarity	NPC159456
0.8182	Intermediate Similarity	NPC46570
0.8182	Intermediate Similarity	NPC4021
0.8182	Intermediate Similarity	NPC67569
0.8174	Intermediate Similarity	NPC137917
0.8167	Intermediate Similarity	NPC122971
0.8167	Intermediate Similarity	NPC197003
0.8167	Intermediate Similarity	NPC190939
0.816	Intermediate Similarity	NPC471352
0.816	Intermediate Similarity	NPC469755
0.816	Intermediate Similarity	NPC469753
0.816	Intermediate Similarity	NPC329986
0.816	Intermediate Similarity	NPC10823
0.816	Intermediate Similarity	NPC140092
0.816	Intermediate Similarity	NPC180079
0.816	Intermediate Similarity	NPC471361
0.816	Intermediate Similarity	NPC86159
0.816	Intermediate Similarity	NPC251866
0.816	Intermediate Similarity	NPC284406
0.816	Intermediate Similarity	NPC17896
0.816	Intermediate Similarity	NPC70542
0.816	Intermediate Similarity	NPC89514
0.816	Intermediate Similarity	NPC232785
0.816	Intermediate Similarity	NPC9499
0.816	Intermediate Similarity	NPC6108
0.816	Intermediate Similarity	NPC125077
0.816	Intermediate Similarity	NPC469751
0.816	Intermediate Similarity	NPC219085
0.816	Intermediate Similarity	NPC469754
0.816	Intermediate Similarity	NPC471360
0.816	Intermediate Similarity	NPC276838
0.816	Intermediate Similarity	NPC469752
0.816	Intermediate Similarity	NPC188234
0.816	Intermediate Similarity	NPC471359
0.816	Intermediate Similarity	NPC471358
0.816	Intermediate Similarity	NPC197707
0.8151	Intermediate Similarity	NPC203862
0.8151	Intermediate Similarity	NPC55296
0.8151	Intermediate Similarity	NPC473405
0.8145	Intermediate Similarity	NPC298841
0.8136	Intermediate Similarity	NPC110861
0.8136	Intermediate Similarity	NPC474557
0.8136	Intermediate Similarity	NPC181145
0.813	Intermediate Similarity	NPC469841
0.813	Intermediate Similarity	NPC473474
0.813	Intermediate Similarity	NPC469842
0.8125	Intermediate Similarity	NPC158350
0.8125	Intermediate Similarity	NPC194716
0.812	Intermediate Similarity	NPC195132
0.812	Intermediate Similarity	NPC64106
0.812	Intermediate Similarity	NPC80843
0.812	Intermediate Similarity	NPC212968
0.812	Intermediate Similarity	NPC65590
0.812	Intermediate Similarity	NPC1046
0.812	Intermediate Similarity	NPC130427
0.812	Intermediate Similarity	NPC161434
0.812	Intermediate Similarity	NPC470543
0.812	Intermediate Similarity	NPC236217
0.812	Intermediate Similarity	NPC48249
0.812	Intermediate Similarity	NPC125923
0.8115	Intermediate Similarity	NPC269642
0.8115	Intermediate Similarity	NPC28532
0.8115	Intermediate Similarity	NPC107493
0.8103	Intermediate Similarity	NPC242611
0.8103	Intermediate Similarity	NPC78046
0.8103	Intermediate Similarity	NPC274507
0.8103	Intermediate Similarity	NPC269095
0.8103	Intermediate Similarity	NPC220984
0.8099	Intermediate Similarity	NPC308459
0.8099	Intermediate Similarity	NPC48692
0.8099	Intermediate Similarity	NPC473130

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 NPC232258 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	255
0.1-0.2	1883
0.2-0.3	3850
0.3-0.4	2063
0.4-0.5	582
0.5-0.6	273
0.6-0.7	196
0.7-0.8	47
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8333	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.816	Intermediate Similarity	NPD7319	Approved
0.8087	Intermediate Similarity	NPD6686	Approved
0.8065	Intermediate Similarity	NPD7507	Approved
0.8051	Intermediate Similarity	NPD8133	Approved
0.8033	Intermediate Similarity	NPD8033	Approved
0.8	Intermediate Similarity	NPD6412	Phase 2
0.8	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.7951	Intermediate Similarity	NPD8377	Approved
0.7951	Intermediate Similarity	NPD8294	Approved
0.7903	Intermediate Similarity	NPD8328	Phase 3
0.7886	Intermediate Similarity	NPD8378	Approved
0.7886	Intermediate Similarity	NPD7503	Approved
0.7886	Intermediate Similarity	NPD8296	Approved
0.7886	Intermediate Similarity	NPD8380	Approved
0.7886	Intermediate Similarity	NPD8335	Approved
0.7886	Intermediate Similarity	NPD8379	Approved
0.7851	Intermediate Similarity	NPD7115	Discovery
0.7787	Intermediate Similarity	NPD7328	Approved
0.7787	Intermediate Similarity	NPD7327	Approved
0.7742	Intermediate Similarity	NPD8513	Phase 3
0.7724	Intermediate Similarity	NPD7516	Approved
0.7656	Intermediate Similarity	NPD7736	Approved
0.76	Intermediate Similarity	NPD8516	Approved
0.76	Intermediate Similarity	NPD8515	Approved
0.76	Intermediate Similarity	NPD8517	Approved
0.7578	Intermediate Similarity	NPD8293	Discontinued
0.7417	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7402	Intermediate Similarity	NPD6370	Approved
0.7287	Intermediate Similarity	NPD7492	Approved
0.7244	Intermediate Similarity	NPD6319	Approved
0.7244	Intermediate Similarity	NPD6054	Approved
0.7244	Intermediate Similarity	NPD6059	Approved
0.7241	Intermediate Similarity	NPD7638	Approved
0.7231	Intermediate Similarity	NPD6616	Approved
0.7227	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7213	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.7179	Intermediate Similarity	NPD7639	Approved
0.7179	Intermediate Similarity	NPD7640	Approved
0.7176	Intermediate Similarity	NPD7078	Approved
0.7154	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7097	Intermediate Similarity	NPD8297	Approved
0.7097	Intermediate Similarity	NPD6882	Approved
0.7059	Intermediate Similarity	NPD7632	Discontinued
0.7054	Intermediate Similarity	NPD6015	Approved
0.7054	Intermediate Similarity	NPD6016	Approved
0.7008	Intermediate Similarity	NPD6009	Approved
0.7	Intermediate Similarity	NPD5988	Approved
0.6967	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.696	Remote Similarity	NPD6053	Discontinued
0.6957	Remote Similarity	NPD6399	Phase 3
0.6949	Remote Similarity	NPD4225	Approved
0.693	Remote Similarity	NPD6698	Approved
0.693	Remote Similarity	NPD46	Approved
0.6911	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6905	Remote Similarity	NPD4632	Approved
0.6897	Remote Similarity	NPD7748	Approved
0.6885	Remote Similarity	NPD6402	Approved
0.6885	Remote Similarity	NPD5739	Approved
0.6885	Remote Similarity	NPD7128	Approved
0.6885	Remote Similarity	NPD6675	Approved
0.6864	Remote Similarity	NPD7902	Approved
0.6855	Remote Similarity	NPD6372	Approved
0.6855	Remote Similarity	NPD6373	Approved
0.6818	Remote Similarity	NPD6067	Discontinued
0.68	Remote Similarity	NPD6371	Approved
0.6791	Remote Similarity	NPD8074	Phase 3
0.6774	Remote Similarity	NPD6881	Approved
0.6774	Remote Similarity	NPD6899	Approved
0.6774	Remote Similarity	NPD7320	Approved
0.6746	Remote Similarity	NPD6649	Approved
0.6746	Remote Similarity	NPD6650	Approved
0.6746	Remote Similarity	NPD8130	Phase 1
0.6741	Remote Similarity	NPD6033	Approved
0.6724	Remote Similarity	NPD7515	Phase 2
0.6723	Remote Similarity	NPD6084	Phase 2
0.6723	Remote Similarity	NPD6083	Phase 2
0.6695	Remote Similarity	NPD5695	Phase 3
0.6694	Remote Similarity	NPD5701	Approved
0.6694	Remote Similarity	NPD5697	Approved
0.6694	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7290	Approved
0.6667	Remote Similarity	NPD7102	Approved
0.6667	Remote Similarity	NPD4634	Approved
0.6667	Remote Similarity	NPD6883	Approved
0.6667	Remote Similarity	NPD8171	Discontinued
0.6618	Remote Similarity	NPD8336	Approved
0.6618	Remote Similarity	NPD8337	Approved
0.6614	Remote Similarity	NPD6617	Approved
0.6614	Remote Similarity	NPD6869	Approved
0.6614	Remote Similarity	NPD6847	Approved
0.6613	Remote Similarity	NPD6008	Approved
0.661	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.661	Remote Similarity	NPD7900	Approved
0.6594	Remote Similarity	NPD7260	Phase 2
0.6587	Remote Similarity	NPD6013	Approved
0.6587	Remote Similarity	NPD6014	Approved
0.6587	Remote Similarity	NPD6012	Approved
0.6581	Remote Similarity	NPD6411	Approved
0.6581	Remote Similarity	NPD8035	Phase 2
0.6581	Remote Similarity	NPD8034	Phase 2
0.6567	Remote Similarity	NPD7604	Phase 2
0.6552	Remote Similarity	NPD5328	Approved
0.6549	Remote Similarity	NPD4786	Approved
0.6547	Remote Similarity	NPD6845	Suspended
0.6541	Remote Similarity	NPD5983	Phase 2
0.6529	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6525	Remote Similarity	NPD5778	Approved
0.6525	Remote Similarity	NPD5779	Approved
0.6508	Remote Similarity	NPD6011	Approved
0.6493	Remote Similarity	NPD8080	Discontinued
0.6484	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD6336	Discontinued
0.6466	Remote Similarity	NPD6672	Approved
0.6466	Remote Similarity	NPD5737	Approved
0.6466	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.6446	Remote Similarity	NPD4755	Approved
0.6444	Remote Similarity	NPD7829	Approved
0.6444	Remote Similarity	NPD7830	Approved
0.6441	Remote Similarity	NPD6079	Approved
0.6441	Remote Similarity	NPD7983	Approved
0.6441	Remote Similarity	NPD7637	Suspended
0.6435	Remote Similarity	NPD7334	Approved
0.6435	Remote Similarity	NPD6409	Approved
0.6435	Remote Similarity	NPD7521	Approved
0.6435	Remote Similarity	NPD7146	Approved
0.6435	Remote Similarity	NPD5330	Approved
0.6435	Remote Similarity	NPD6684	Approved
0.6435	Remote Similarity	NPD3618	Phase 1
0.6429	Remote Similarity	NPD8338	Approved
0.642	Remote Similarity	NPD7799	Discontinued
0.6419	Remote Similarity	NPD7625	Phase 1
0.6418	Remote Similarity	NPD6921	Approved
0.6412	Remote Similarity	NPD6940	Discontinued
0.641	Remote Similarity	NPD6101	Approved
0.641	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6403	Remote Similarity	NPD5956	Approved
0.6393	Remote Similarity	NPD5696	Approved
0.6387	Remote Similarity	NPD4202	Approved
0.6372	Remote Similarity	NPD3667	Approved
0.6371	Remote Similarity	NPD5211	Phase 2
0.6364	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6356	Remote Similarity	NPD7838	Discovery
0.6356	Remote Similarity	NPD5785	Approved
0.6348	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD5286	Approved
0.6341	Remote Similarity	NPD5285	Approved
0.6341	Remote Similarity	NPD4700	Approved
0.6341	Remote Similarity	NPD4696	Approved
0.6325	Remote Similarity	NPD6903	Approved
0.6324	Remote Similarity	NPD7642	Approved
0.6303	Remote Similarity	NPD5693	Phase 1
0.6303	Remote Similarity	NPD5281	Approved
0.6303	Remote Similarity	NPD5284	Approved
0.6296	Remote Similarity	NPD8444	Approved
0.6296	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6293	Remote Similarity	NPD5279	Phase 3
0.629	Remote Similarity	NPD5344	Discontinued
0.6288	Remote Similarity	NPD6274	Approved
0.6271	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6271	Remote Similarity	NPD4753	Phase 2
0.627	Remote Similarity	NPD5141	Approved
0.6269	Remote Similarity	NPD7100	Approved
0.6269	Remote Similarity	NPD7101	Approved
0.6261	Remote Similarity	NPD3665	Phase 1
0.6261	Remote Similarity	NPD3133	Approved
0.6261	Remote Similarity	NPD3666	Approved
0.624	Remote Similarity	NPD5225	Approved
0.624	Remote Similarity	NPD5226	Approved
0.624	Remote Similarity	NPD5224	Approved
0.624	Remote Similarity	NPD4633	Approved
0.6232	Remote Similarity	NPD8451	Approved
0.623	Remote Similarity	NPD4697	Phase 3
0.623	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.623	Remote Similarity	NPD5222	Approved
0.623	Remote Similarity	NPD5221	Approved
0.622	Remote Similarity	NPD4767	Approved
0.622	Remote Similarity	NPD4768	Approved
0.6207	Remote Similarity	NPD1694	Approved
0.6197	Remote Similarity	NPD8449	Approved
0.6194	Remote Similarity	NPD6335	Approved
0.619	Remote Similarity	NPD5175	Approved
0.619	Remote Similarity	NPD5174	Approved
0.6187	Remote Similarity	NPD8448	Approved
0.6179	Remote Similarity	NPD5173	Approved
0.6176	Remote Similarity	NPD6908	Approved
0.6176	Remote Similarity	NPD6909	Approved
0.617	Remote Similarity	NPD8390	Approved
0.617	Remote Similarity	NPD6914	Discontinued
0.617	Remote Similarity	NPD8392	Approved
0.617	Remote Similarity	NPD8391	Approved
0.6167	Remote Similarity	NPD6050	Approved
0.6165	Remote Similarity	NPD6868	Approved
0.6161	Remote Similarity	NPD6115	Approved
0.6161	Remote Similarity	NPD6114	Approved
0.6161	Remote Similarity	NPD6697	Approved
0.6161	Remote Similarity	NPD6118	Approved
0.616	Remote Similarity	NPD5223	Approved
0.6154	Remote Similarity	NPD3574	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