NPASS Compound

Structure

CID129434 OpenBabel06191715482D 44 49 0 0 1 0 0 0 0 0999 V2000 -4.0293 -2.3263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1778 2.0982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8499 1.0960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8814 3.0814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7333 3.5732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5856 0.1296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7332 0.6218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1778 0.1317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9943 0.1298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1416 -1.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2898 2.0978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4748 0.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3263 -1.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0293 -1.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0293 1.6066 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1778 -0.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9940 -0.8540 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.4375 0.6214 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4374 1.6057 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.1422 0.6214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8808 2.0982 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5851 2.0978 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.1422 1.6057 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.2896 -0.8544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0293 0.6233 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9832 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.2898 0.1293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4748 -0.8515 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9832 -1.7030 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -1.7030 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8808 -0.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4916 -0.8515 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7332 1.6060 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9832 1.7030 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.8600 -1.3541 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.0082 2.1057 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4235 -1.3544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4581 -0.8515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4748 -2.5545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4916 -2.5545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7323 -1.3431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4748 -0.8515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8808 0.1317 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 14 1 0 0 0 0 4 5 1 0 0 0 0 4 21 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 7 33 1 0 0 0 0 8 16 1 0 0 0 0 8 25 1 0 0 0 0 9 17 1 0 0 0 0 9 20 1 0 0 0 0 10 17 1 0 0 0 0 10 24 1 0 0 0 0 11 23 1 0 0 0 0 12 34 1 0 0 0 0 13 16 1 0 0 0 0 13 42 1 0 0 0 0 14 16 2 0 0 0 0 14 31 1 0 0 0 0 15 2 1 6 0 0 0 15 21 1 0 0 0 0 17 35 1 6 0 0 0 18 6 1 6 0 0 0 18 19 1 0 0 0 0 18 27 1 0 0 0 0 19 11 1 1 0 0 0 19 22 1 0 0 0 0 20 23 1 0 0 0 0 20 27 2 0 0 0 0 21 33 1 6 0 0 0 22 33 1 6 0 0 0 23 36 1 1 0 0 0 24 27 1 0 0 0 0 24 37 2 0 0 0 0 25 15 1 1 0 0 0 25 43 1 0 0 0 0 26 12 1 6 0 0 0 26 28 1 0 0 0 0 26 44 1 0 0 0 0 28 29 1 0 0 0 0 28 38 1 1 0 0 0 29 30 1 0 0 0 0 29 39 1 6 0 0 0 30 32 1 0 0 0 0 30 40 1 1 0 0 0 31 41 2 0 0 0 0 31 43 1 0 0 0 0 32 42 1 6 0 0 0 32 44 1 0 0 0 0 33 3 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	620.32
Volume:	614.132
LogP:	1.472
LogD:	1.362
LogS:	-3.258
# Rotatable Bonds:	6
TPSA:	180.05
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	6
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.268
Synthetic Accessibility Score:	5.585
Fsp3:	0.848
Lipinski Rule-of-5:	Rejected
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:	-5.737
MDCK Permeability:	5.108046025270596e-05
Pgp-inhibitor:	0.459
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.937
20% Bioavailability (F20%):	0.044
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.038
Plasma Protein Binding (PPB):	77.1834487915039%
Volume Distribution (VD):	0.731
Pgp-substrate:	8.742777824401855%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.102
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.339
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.048
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.06
CYP3A4-inhibitor:	0.213
CYP3A4-substrate:	0.5

ADMET: Excretion

Clearance (CL):	3.842
Half-life (T1/2):	0.822

ADMET: Toxicity

hERG Blockers:	0.22
Human Hepatotoxicity (H-HT):	0.266
Drug-inuced Liver Injury (DILI):	0.474
AMES Toxicity:	0.048
Rat Oral Acute Toxicity:	0.813
Maximum Recommended Daily Dose:	0.929
Skin Sensitization:	0.03
Carcinogencity:	0.329
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.05

Download Data

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

Natural Product: NPC129434

Natural Product ID:	NPC129434
*Common Name:**	Withalongolide L
IUPAC Name:	(2R)-2-[(1S)-1-[(3R,6S,8S,9S,13S,14S,17R)-3,6-dihydroxy-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 L
Standard InCHIKey:	DKRAEDZNHJHJAB-YJKJOOOHSA-N
Standard InCHI:	InChI=1S/C33H48O11/c1-14-16(13-42-32-30(40)29(39)28(38)26(12-34)44-32)8-25(43-31(14)41)15(2)21-4-5-22-19-11-23(36)20-9-17(35)10-24(37)27(20)18(19)6-7-33(21,22)3/h15,17-19,21-23,25-26,28-30,32,34-36,38-40H,4-13H2,1-3H3/t15-,17+,18-,19+,21+,22-,23-,25+,26+,28+,29-,30+,32+,33+/m0/s1
SMILES:	OC[C@H]1O[C@@H](OCC2=C(C)C(=O)O[C@H](C2)[C@H]([C@H]2CC[C@@H]3[C@]2(C)CC[C@H]2[C@H]3C[C@@H](C3=C2C(=O)C[C@@H](C3)O)O)C)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1934464
PubChem CID:	56926208
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[510084]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	IC50	>	10000.0	nM	PMID[510084]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[510084]
NPT27	Others	Unspecified		IC50	>	10000.0	nM	PMID[510084]

☑ 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 NPC129434 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	273
0.1-0.2	1570
0.2-0.3	4839
0.3-0.4	8789
0.4-0.5	11393
0.5-0.6	7177
0.6-0.7	5841
0.7-0.8	2662
0.8-0.85	134
0.85-0.9	14
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.982	High Similarity	NPC232258
0.9554	High Similarity	NPC291564
0.9322	High Similarity	NPC245094
0.9231	High Similarity	NPC318135
0.9091	High Similarity	NPC231240
0.9083	High Similarity	NPC476966
0.9016	High Similarity	NPC316915
0.9008	High Similarity	NPC173347
0.8974	High Similarity	NPC202051
0.8974	High Similarity	NPC476204
0.8974	High Similarity	NPC170084
0.885	High Similarity	NPC477073
0.8839	High Similarity	NPC477069
0.8839	High Similarity	NPC477070
0.8772	High Similarity	NPC477253
0.8772	High Similarity	NPC233003
0.8707	High Similarity	NPC207637
0.8696	High Similarity	NPC477074
0.8696	High Similarity	NPC251309
0.8689	High Similarity	NPC311534
0.8644	High Similarity	NPC477071
0.8632	High Similarity	NPC477252
0.8621	High Similarity	NPC220293
0.8618	High Similarity	NPC473593
0.8596	High Similarity	NPC129340
0.8584	High Similarity	NPC195708
0.8571	High Similarity	NPC476127
0.8571	High Similarity	NPC476150
0.8571	High Similarity	NPC470312
0.8559	High Similarity	NPC473828
0.8559	High Similarity	NPC239293
0.8559	High Similarity	NPC473617
0.8509	High Similarity	NPC31522
0.8509	High Similarity	NPC265655
0.85	High Similarity	NPC187950
0.85	High Similarity	NPC278163
0.8475	Intermediate Similarity	NPC474483
0.8468	Intermediate Similarity	NPC471407
0.8462	Intermediate Similarity	NPC116024
0.8462	Intermediate Similarity	NPC473882
0.8455	Intermediate Similarity	NPC42399
0.8443	Intermediate Similarity	NPC3381
0.8435	Intermediate Similarity	NPC90630
0.8435	Intermediate Similarity	NPC475243
0.843	Intermediate Similarity	NPC23786
0.843	Intermediate Similarity	NPC470265
0.8421	Intermediate Similarity	NPC90946
0.8421	Intermediate Similarity	NPC300614
0.8376	Intermediate Similarity	NPC260665
0.8374	Intermediate Similarity	NPC174367
0.8374	Intermediate Similarity	NPC47113
0.8362	Intermediate Similarity	NPC250481
0.8362	Intermediate Similarity	NPC285410
0.8362	Intermediate Similarity	NPC292196
0.8362	Intermediate Similarity	NPC263827
0.8348	Intermediate Similarity	NPC475364
0.8347	Intermediate Similarity	NPC159456
0.8347	Intermediate Similarity	NPC4021
0.8347	Intermediate Similarity	NPC46570
0.8347	Intermediate Similarity	NPC67569
0.8333	Intermediate Similarity	NPC474179
0.8333	Intermediate Similarity	NPC122971
0.8333	Intermediate Similarity	NPC475834
0.8333	Intermediate Similarity	NPC471855
0.8319	Intermediate Similarity	NPC55296
0.8319	Intermediate Similarity	NPC223741
0.8306	Intermediate Similarity	NPC117702
0.8306	Intermediate Similarity	NPC471357
0.8306	Intermediate Similarity	NPC146456
0.8306	Intermediate Similarity	NPC469757
0.8306	Intermediate Similarity	NPC240070
0.8306	Intermediate Similarity	NPC470516
0.8306	Intermediate Similarity	NPC329784
0.8305	Intermediate Similarity	NPC181145
0.8305	Intermediate Similarity	NPC74727
0.8305	Intermediate Similarity	NPC475163
0.8293	Intermediate Similarity	NPC130229
0.8293	Intermediate Similarity	NPC7850
0.8293	Intermediate Similarity	NPC6615
0.8291	Intermediate Similarity	NPC474265
0.8291	Intermediate Similarity	NPC210420
0.8291	Intermediate Similarity	NPC471967
0.8279	Intermediate Similarity	NPC107493
0.8279	Intermediate Similarity	NPC28532
0.8279	Intermediate Similarity	NPC269642
0.8276	Intermediate Similarity	NPC52241
0.8276	Intermediate Similarity	NPC475317
0.8276	Intermediate Similarity	NPC27551
0.8276	Intermediate Similarity	NPC114961
0.8276	Intermediate Similarity	NPC154856
0.8276	Intermediate Similarity	NPC83005
0.8268	Intermediate Similarity	NPC247190
0.8268	Intermediate Similarity	NPC146857
0.8268	Intermediate Similarity	NPC116075
0.8268	Intermediate Similarity	NPC469749
0.8268	Intermediate Similarity	NPC32793
0.8264	Intermediate Similarity	NPC48692
0.8264	Intermediate Similarity	NPC268530
0.8264	Intermediate Similarity	NPC251226
0.8264	Intermediate Similarity	NPC129393
0.8264	Intermediate Similarity	NPC154491
0.8264	Intermediate Similarity	NPC281840
0.8264	Intermediate Similarity	NPC476849
0.8261	Intermediate Similarity	NPC325054
0.8261	Intermediate Similarity	NPC295389
0.8261	Intermediate Similarity	NPC285576
0.825	Intermediate Similarity	NPC475913
0.825	Intermediate Similarity	NPC45475
0.8246	Intermediate Similarity	NPC162033
0.824	Intermediate Similarity	NPC112492
0.824	Intermediate Similarity	NPC472269
0.824	Intermediate Similarity	NPC473620
0.824	Intermediate Similarity	NPC472268
0.824	Intermediate Similarity	NPC472270
0.824	Intermediate Similarity	NPC23020
0.8235	Intermediate Similarity	NPC469823
0.8235	Intermediate Similarity	NPC469820
0.823	Intermediate Similarity	NPC159533
0.822	Intermediate Similarity	NPC264153
0.822	Intermediate Similarity	NPC75167
0.822	Intermediate Similarity	NPC473159
0.822	Intermediate Similarity	NPC73986
0.822	Intermediate Similarity	NPC311592
0.8211	Intermediate Similarity	NPC27363
0.8211	Intermediate Similarity	NPC469789
0.8211	Intermediate Similarity	NPC41129
0.8205	Intermediate Similarity	NPC190837
0.8205	Intermediate Similarity	NPC11035
0.8205	Intermediate Similarity	NPC31839
0.8203	Intermediate Similarity	NPC329636
0.8197	Intermediate Similarity	NPC131841
0.8197	Intermediate Similarity	NPC169727
0.8197	Intermediate Similarity	NPC47567
0.8197	Intermediate Similarity	NPC412
0.8197	Intermediate Similarity	NPC258815
0.8197	Intermediate Similarity	NPC194310
0.8197	Intermediate Similarity	NPC475182
0.8197	Intermediate Similarity	NPC241310
0.8197	Intermediate Similarity	NPC258789
0.819	Intermediate Similarity	NPC246205
0.819	Intermediate Similarity	NPC137917
0.819	Intermediate Similarity	NPC118225
0.8189	Intermediate Similarity	NPC319719
0.8189	Intermediate Similarity	NPC196874
0.8189	Intermediate Similarity	NPC322904
0.8189	Intermediate Similarity	NPC324933
0.8189	Intermediate Similarity	NPC475444
0.8189	Intermediate Similarity	NPC473679
0.8189	Intermediate Similarity	NPC183816
0.8189	Intermediate Similarity	NPC475177
0.8189	Intermediate Similarity	NPC233223
0.8182	Intermediate Similarity	NPC258592
0.8182	Intermediate Similarity	NPC230513
0.8182	Intermediate Similarity	NPC178548
0.8182	Intermediate Similarity	NPC473274
0.8175	Intermediate Similarity	NPC477235
0.8175	Intermediate Similarity	NPC469755
0.8175	Intermediate Similarity	NPC6108
0.8175	Intermediate Similarity	NPC10823
0.8175	Intermediate Similarity	NPC471359
0.8175	Intermediate Similarity	NPC125077
0.8175	Intermediate Similarity	NPC471352
0.8175	Intermediate Similarity	NPC251866
0.8175	Intermediate Similarity	NPC219085
0.8175	Intermediate Similarity	NPC469752
0.8175	Intermediate Similarity	NPC232785
0.8175	Intermediate Similarity	NPC17896
0.8175	Intermediate Similarity	NPC469751
0.8175	Intermediate Similarity	NPC471358
0.8175	Intermediate Similarity	NPC197707
0.8175	Intermediate Similarity	NPC180079
0.8175	Intermediate Similarity	NPC469753
0.8175	Intermediate Similarity	NPC329986
0.8175	Intermediate Similarity	NPC469754
0.8175	Intermediate Similarity	NPC276838
0.8175	Intermediate Similarity	NPC471361
0.8175	Intermediate Similarity	NPC284406
0.8175	Intermediate Similarity	NPC86159
0.8175	Intermediate Similarity	NPC70542
0.8175	Intermediate Similarity	NPC140092
0.8175	Intermediate Similarity	NPC89514
0.8175	Intermediate Similarity	NPC9499
0.8175	Intermediate Similarity	NPC471360
0.8175	Intermediate Similarity	NPC188234
0.8167	Intermediate Similarity	NPC473405
0.8167	Intermediate Similarity	NPC203862
0.8167	Intermediate Similarity	NPC473968
0.816	Intermediate Similarity	NPC298841
0.8151	Intermediate Similarity	NPC474557
0.8151	Intermediate Similarity	NPC472274
0.8151	Intermediate Similarity	NPC165439
0.8151	Intermediate Similarity	NPC110861
0.8145	Intermediate Similarity	NPC30188
0.8145	Intermediate Similarity	NPC470922
0.8145	Intermediate Similarity	NPC177820
0.8145	Intermediate Similarity	NPC248202
0.814	Intermediate Similarity	NPC194716
0.814	Intermediate Similarity	NPC158350
0.8136	Intermediate Similarity	NPC48249
0.8136	Intermediate Similarity	NPC174836

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 NPC129434 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	1880
0.2-0.3	3824
0.3-0.4	2084
0.4-0.5	587
0.5-0.6	275
0.6-0.7	201
0.7-0.8	44
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
0.8348	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.8175	Intermediate Similarity	NPD7319	Approved
0.808	Intermediate Similarity	NPD7507	Approved
0.8049	Intermediate Similarity	NPD8033	Approved
0.8017	Intermediate Similarity	NPD7115	Discovery
0.8017	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.7967	Intermediate Similarity	NPD8377	Approved
0.7967	Intermediate Similarity	NPD8294	Approved
0.7949	Intermediate Similarity	NPD6686	Approved
0.792	Intermediate Similarity	NPD8328	Phase 3
0.7917	Intermediate Similarity	NPD8133	Approved
0.7903	Intermediate Similarity	NPD8380	Approved
0.7903	Intermediate Similarity	NPD8379	Approved
0.7903	Intermediate Similarity	NPD7503	Approved
0.7903	Intermediate Similarity	NPD8335	Approved
0.7903	Intermediate Similarity	NPD8378	Approved
0.7903	Intermediate Similarity	NPD8513	Phase 3
0.7903	Intermediate Similarity	NPD8296	Approved
0.7863	Intermediate Similarity	NPD6412	Phase 2
0.7805	Intermediate Similarity	NPD7328	Approved
0.7805	Intermediate Similarity	NPD7327	Approved
0.776	Intermediate Similarity	NPD8516	Approved
0.776	Intermediate Similarity	NPD8517	Approved
0.776	Intermediate Similarity	NPD8515	Approved
0.7742	Intermediate Similarity	NPD7516	Approved
0.7674	Intermediate Similarity	NPD7736	Approved
0.7597	Intermediate Similarity	NPD8293	Discontinued
0.7438	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7422	Intermediate Similarity	NPD6370	Approved
0.735	Intermediate Similarity	NPD7640	Approved
0.735	Intermediate Similarity	NPD7639	Approved
0.7308	Intermediate Similarity	NPD7492	Approved
0.7266	Intermediate Similarity	NPD6059	Approved
0.7266	Intermediate Similarity	NPD6319	Approved
0.7266	Intermediate Similarity	NPD6054	Approved
0.7265	Intermediate Similarity	NPD7638	Approved
0.7252	Intermediate Similarity	NPD6616	Approved
0.7236	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.7227	Intermediate Similarity	NPD7632	Discontinued
0.7197	Intermediate Similarity	NPD7078	Approved
0.7177	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.712	Intermediate Similarity	NPD8297	Approved
0.712	Intermediate Similarity	NPD6882	Approved
0.7119	Intermediate Similarity	NPD4225	Approved
0.7107	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7077	Intermediate Similarity	NPD6016	Approved
0.7077	Intermediate Similarity	NPD6015	Approved
0.7031	Intermediate Similarity	NPD6009	Approved
0.7023	Intermediate Similarity	NPD5988	Approved
0.6992	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.694	Remote Similarity	NPD8074	Phase 3
0.6935	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6929	Remote Similarity	NPD4632	Approved
0.6923	Remote Similarity	NPD7748	Approved
0.6911	Remote Similarity	NPD6675	Approved
0.6911	Remote Similarity	NPD7128	Approved
0.6911	Remote Similarity	NPD5739	Approved
0.6911	Remote Similarity	NPD6402	Approved
0.6891	Remote Similarity	NPD7902	Approved
0.688	Remote Similarity	NPD6373	Approved
0.688	Remote Similarity	NPD6372	Approved
0.685	Remote Similarity	NPD6053	Discontinued
0.6842	Remote Similarity	NPD6067	Discontinued
0.6838	Remote Similarity	NPD6399	Phase 3
0.6825	Remote Similarity	NPD6371	Approved
0.681	Remote Similarity	NPD6698	Approved
0.681	Remote Similarity	NPD46	Approved
0.68	Remote Similarity	NPD6899	Approved
0.68	Remote Similarity	NPD7320	Approved
0.68	Remote Similarity	NPD6881	Approved
0.6772	Remote Similarity	NPD8130	Phase 1
0.6772	Remote Similarity	NPD6649	Approved
0.6772	Remote Similarity	NPD6650	Approved
0.6765	Remote Similarity	NPD6033	Approved
0.6752	Remote Similarity	NPD7515	Phase 2
0.672	Remote Similarity	NPD5697	Approved
0.672	Remote Similarity	NPD5701	Approved
0.6693	Remote Similarity	NPD6883	Approved
0.6693	Remote Similarity	NPD7290	Approved
0.6693	Remote Similarity	NPD4634	Approved
0.6693	Remote Similarity	NPD7102	Approved
0.6641	Remote Similarity	NPD6869	Approved
0.6641	Remote Similarity	NPD6847	Approved
0.6641	Remote Similarity	NPD6617	Approved
0.664	Remote Similarity	NPD6008	Approved
0.6639	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.6639	Remote Similarity	NPD7900	Approved
0.6619	Remote Similarity	NPD7260	Phase 2
0.6614	Remote Similarity	NPD6014	Approved
0.6614	Remote Similarity	NPD6013	Approved
0.6614	Remote Similarity	NPD6012	Approved
0.6612	Remote Similarity	NPD6083	Phase 2
0.6612	Remote Similarity	NPD6084	Phase 2
0.661	Remote Similarity	NPD8035	Phase 2
0.661	Remote Similarity	NPD8034	Phase 2
0.6593	Remote Similarity	NPD7604	Phase 2
0.6587	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6583	Remote Similarity	NPD5695	Phase 3
0.6581	Remote Similarity	NPD5328	Approved
0.6571	Remote Similarity	NPD6845	Suspended
0.6567	Remote Similarity	NPD5983	Phase 2
0.6557	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6555	Remote Similarity	NPD5778	Approved
0.6555	Remote Similarity	NPD5779	Approved
0.6555	Remote Similarity	NPD8171	Discontinued
0.6535	Remote Similarity	NPD6011	Approved
0.6532	Remote Similarity	NPD5211	Phase 2
0.6522	Remote Similarity	NPD8336	Approved
0.6522	Remote Similarity	NPD8337	Approved
0.6512	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6496	Remote Similarity	NPD6336	Discontinued
0.6475	Remote Similarity	NPD4755	Approved
0.6471	Remote Similarity	NPD6079	Approved
0.6471	Remote Similarity	NPD6411	Approved
0.6471	Remote Similarity	NPD7983	Approved
0.6471	Remote Similarity	NPD7637	Suspended
0.6466	Remote Similarity	NPD3618	Phase 1
0.6454	Remote Similarity	NPD8338	Approved
0.6452	Remote Similarity	NPD5344	Discontinued
0.6444	Remote Similarity	NPD6921	Approved
0.6443	Remote Similarity	NPD7625	Phase 1
0.6442	Remote Similarity	NPD7799	Discontinued
0.6435	Remote Similarity	NPD4786	Approved
0.6435	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD5141	Approved
0.6417	Remote Similarity	NPD4202	Approved
0.6397	Remote Similarity	NPD8080	Discontinued
0.6387	Remote Similarity	NPD5785	Approved
0.6379	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6371	Remote Similarity	NPD5285	Approved
0.6371	Remote Similarity	NPD4700	Approved
0.6371	Remote Similarity	NPD4696	Approved
0.6371	Remote Similarity	NPD5286	Approved
0.6356	Remote Similarity	NPD6672	Approved
0.6356	Remote Similarity	NPD5737	Approved
0.6356	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.635	Remote Similarity	NPD7830	Approved
0.635	Remote Similarity	NPD7829	Approved
0.6325	Remote Similarity	NPD5330	Approved
0.6325	Remote Similarity	NPD7334	Approved
0.6325	Remote Similarity	NPD7146	Approved
0.6325	Remote Similarity	NPD6684	Approved
0.6325	Remote Similarity	NPD6409	Approved
0.6325	Remote Similarity	NPD7521	Approved
0.6316	Remote Similarity	NPD6274	Approved
0.6316	Remote Similarity	NPD6940	Discontinued
0.6312	Remote Similarity	NPD5956	Approved
0.6303	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6303	Remote Similarity	NPD6101	Approved
0.6296	Remote Similarity	NPD7101	Approved
0.6296	Remote Similarity	NPD7100	Approved
0.629	Remote Similarity	NPD5696	Approved
0.627	Remote Similarity	NPD5225	Approved
0.627	Remote Similarity	NPD4633	Approved
0.627	Remote Similarity	NPD5224	Approved
0.627	Remote Similarity	NPD5226	Approved
0.6269	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6261	Remote Similarity	NPD3667	Approved
0.626	Remote Similarity	NPD4697	Phase 3
0.626	Remote Similarity	NPD5222	Approved
0.626	Remote Similarity	NPD5221	Approved
0.626	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.625	Remote Similarity	NPD4767	Approved
0.625	Remote Similarity	NPD7838	Discovery
0.625	Remote Similarity	NPD4768	Approved
0.6239	Remote Similarity	NPD1694	Approved
0.6232	Remote Similarity	NPD7642	Approved
0.6222	Remote Similarity	NPD6335	Approved
0.622	Remote Similarity	NPD5174	Approved
0.622	Remote Similarity	NPD5175	Approved
0.6218	Remote Similarity	NPD6903	Approved
0.621	Remote Similarity	NPD5173	Approved
0.6204	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6204	Remote Similarity	NPD6908	Approved
0.6204	Remote Similarity	NPD6909	Approved
0.6204	Remote Similarity	NPD8444	Approved
0.6198	Remote Similarity	NPD5281	Approved
0.6198	Remote Similarity	NPD5693	Phase 1
0.6198	Remote Similarity	NPD5284	Approved
0.6197	Remote Similarity	NPD6914	Discontinued
0.6195	Remote Similarity	NPD6114	Approved
0.6195	Remote Similarity	NPD6697	Approved
0.6195	Remote Similarity	NPD6115	Approved
0.6195	Remote Similarity	NPD6118	Approved
0.6194	Remote Similarity	NPD6868	Approved
0.619	Remote Similarity	NPD5223	Approved
0.6186	Remote Similarity	NPD5279	Phase 3
0.6186	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6179	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6167	Remote Similarity	NPD4753	Phase 2
0.6167	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD4729	Approved
0.6154	Remote Similarity	NPD3665	Phase 1
0.6154	Remote Similarity	NPD4730	Approved
0.6154	Remote Similarity	NPD3666	Approved
0.6154	Remote Similarity	NPD3133	Approved
0.6148	Remote Similarity	NPD6317	Approved
0.6143	Remote Similarity	NPD8451	Approved
0.6129	Remote Similarity	NPD7839	Suspended
0.6111	Remote Similarity	NPD8449	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