NPASS Compound

Structure

CID34965 OpenBabel06191715362D 32 34 0 0 1 0 0 0 0 0999 V2000 -8.7648 3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 4.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2872 1.2459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 -0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3007 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0327 2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0327 3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 2.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8366 3.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7026 4.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5686 3.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8090 1.4013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.8988 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 2.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1045 0.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4781 0.6581 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2007 0.8392 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8988 4.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 4.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 5.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4347 4.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0169 2.3794 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8988 1.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3917 0.2514 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7648 2.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 1.4945 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 -4.4347 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 2.4945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 28 1 0 0 0 0 2 3 2 0 0 0 0 2 8 1 0 0 0 0 3 10 1 0 0 0 0 4 8 2 0 0 0 0 4 9 1 0 0 0 0 5 29 1 0 0 0 0 6 19 1 0 0 0 0 6 20 1 0 0 0 0 7 19 1 0 0 0 0 7 30 1 0 0 0 0 8 31 1 0 0 0 0 9 10 2 0 0 0 0 9 16 1 0 0 0 0 10 21 1 0 0 0 0 11 5 1 1 0 0 0 11 12 1 0 0 0 0 11 32 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 6 0 0 0 13 14 1 0 0 0 0 13 23 1 1 0 0 0 14 17 1 0 0 0 0 14 24 1 6 0 0 0 15 18 1 0 0 0 0 15 19 1 6 0 0 0 15 25 1 0 0 0 0 16 26 2 0 0 0 0 16 28 1 0 0 0 0 17 31 1 1 0 0 0 17 32 1 0 0 0 0 18 29 1 1 0 0 0 18 30 1 0 0 0 0 19 27 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.14
Volume:	415.238
LogP:	-0.34
LogD:	-0.471
LogS:	-2.111
# Rotatable Bonds:	8
TPSA:	204.83
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	4.397
Fsp3:	0.632
Lipinski Rule-of-5:	Rejected
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:	-6.605
MDCK Permeability:	5.138545748195611e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.99
Human Intestinal Absorption (HIA):	0.935
20% Bioavailability (F20%):	0.083
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.235
Plasma Protein Binding (PPB):	36.534461975097656%
Volume Distribution (VD):	0.415
Pgp-substrate:	41.12024688720703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.043
CYP1A2-substrate:	0.064
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.136
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.025

ADMET: Excretion

Clearance (CL):	1.482
Half-life (T1/2):	0.806

ADMET: Toxicity

hERG Blockers:	0.196
Human Hepatotoxicity (H-HT):	0.087
Drug-inuced Liver Injury (DILI):	0.549
AMES Toxicity:	0.382
Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.449
Carcinogencity:	0.112
Eye Corrosion:	0.003
Eye Irritation:	0.044
Respiratory Toxicity:	0.027

Download Data

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

Natural Product: NPC34965

Natural Product ID:	NPC34965
*Common Name:**	Saccharumoside C
IUPAC Name:	methyl 5-[(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl]oxy-2-hydroxybenzoate
Synonyms:	Saccharumoside C
Standard InCHIKey:	NIVUGFISTDXAKA-XLBSEFGXSA-N
Standard InCHI:	InChI=1S/C19H26O13/c1-28-16(26)9-4-8(2-3-10(9)21)31-17-14(24)13(23)12(22)11(32-17)5-29-18-15(25)19(27,6-20)7-30-18/h2-4,11-15,17-18,20-25,27H,5-7H2,1H3/t11-,12-,13+,14-,15+,17-,18-,19-/m1/s1
SMILES:	COC(=O)c1cc(ccc1O)O[C@@H]1O[C@H](CO[C@@H]2OC[C@]([C@H]2O)(O)CO)[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1923080
PubChem CID:	56834591
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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
NPO14559	Acer saccharum	Species	Sapindaceae	Eukaryota	bark	n.a.	n.a.	PMID[22032697]
NPO14559	Acer saccharum	Species	Sapindaceae	Eukaryota	n.a.	bark	n.a.	PMID[22032697]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14559	Acer saccharum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15954	Pyrenula japonica	Species	Pyrenulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14559	Acer saccharum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16326	Scopolia parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO619	Ankistrodesmus braunii	Species	Selenastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9141	Epimedium wushanense	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17141	Lonchocarpus longistylus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18071	Euryops pedunculatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14559	Acer saccharum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17917	Thamnophis sirtalis	Species	Colubridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11755	Banisteriopsis caapi	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17600	Gnathotrichus sulcatus	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15594	Aplidiopsis confluata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14001	Ceroplastes pseudoceriferus	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5016	Glossogyne tenuifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16326	Scopolia parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26304	Hymenocallis littoralis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17444	Gleichenia japonica	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15740	Garcinia purpurea	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15954	Pyrenula japonica	Species	Pyrenulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14507.1	Quercus ithaburensis subsp. macrolepis	Subspecies	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12630	Senecio oxyodontus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16049	Cryptocarya pleurosperma	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17757	Plectranthus saccatus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16210	Androcymbium palaestinum	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10751	Bothriocline laxa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16693	Byrsonima crassifolia	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11280	Aphanoascus terreus	Species	Onygenaceae	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	3

Activity Type	# Activity
Cell Line	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[456348]
NPT492	Cell Line	Caco-2	Homo sapiens	IC50	<	5.0	ug.mL-1	PMID[456348]
NPT27	Others	Unspecified		IC50	<	5.0	ug.mL-1	PMID[456348]

☑ 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 NPC34965 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	326
0.1-0.2	1351
0.2-0.3	3287
0.3-0.4	7345
0.4-0.5	10665
0.5-0.6	5270
0.6-0.7	6409
0.7-0.8	7491
0.8-0.85	493
0.85-0.9	42
0.9-0.95	16
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC183536
0.9655	High Similarity	NPC83975
0.94	High Similarity	NPC470331
0.9333	High Similarity	NPC215811
0.931	High Similarity	NPC242756
0.9272	High Similarity	NPC299761
0.9272	High Similarity	NPC92153
0.9272	High Similarity	NPC299435
0.9272	High Similarity	NPC260604
0.9272	High Similarity	NPC279281
0.9272	High Similarity	NPC230439
0.9257	High Similarity	NPC92054
0.9257	High Similarity	NPC4958
0.9257	High Similarity	NPC140722
0.9156	High Similarity	NPC57072
0.9156	High Similarity	NPC231475
0.9091	High Similarity	NPC476026
0.9091	High Similarity	NPC474398
0.9091	High Similarity	NPC474441
0.9091	High Similarity	NPC474401
0.9073	High Similarity	NPC93619
0.9038	High Similarity	NPC217950
0.8917	High Similarity	NPC132737
0.8896	High Similarity	NPC185103
0.8874	High Similarity	NPC302989
0.8868	High Similarity	NPC280923
0.8861	High Similarity	NPC22324
0.8851	High Similarity	NPC164599
0.8851	High Similarity	NPC65833
0.8851	High Similarity	NPC31081
0.8851	High Similarity	NPC245219
0.8846	High Similarity	NPC177742
0.8816	High Similarity	NPC22137
0.8808	High Similarity	NPC474422
0.8805	High Similarity	NPC475183
0.879	High Similarity	NPC279732
0.8766	High Similarity	NPC23253
0.8701	High Similarity	NPC131874
0.8696	High Similarity	NPC475174
0.8688	High Similarity	NPC127415
0.8679	High Similarity	NPC71780
0.8662	High Similarity	NPC149368
0.8662	High Similarity	NPC265480
0.8654	High Similarity	NPC472127
0.8654	High Similarity	NPC472128
0.865	High Similarity	NPC212748
0.865	High Similarity	NPC280385
0.8642	High Similarity	NPC116745
0.8636	High Similarity	NPC104172
0.8636	High Similarity	NPC88886
0.8634	High Similarity	NPC472131
0.8634	High Similarity	NPC472130
0.8634	High Similarity	NPC178281
0.8627	High Similarity	NPC189631
0.8625	High Similarity	NPC61594
0.8625	High Similarity	NPC56735
0.8616	High Similarity	NPC328093
0.8608	High Similarity	NPC43638
0.8606	High Similarity	NPC169645
0.8606	High Similarity	NPC84482
0.86	High Similarity	NPC145319
0.8598	High Similarity	NPC472386
0.8598	High Similarity	NPC254540
0.8598	High Similarity	NPC172807
0.8598	High Similarity	NPC211594
0.8571	High Similarity	NPC94777
0.8571	High Similarity	NPC199335
0.8571	High Similarity	NPC147596
0.8571	High Similarity	NPC17432
0.8571	High Similarity	NPC111785
0.8562	High Similarity	NPC25389
0.8562	High Similarity	NPC311803
0.8562	High Similarity	NPC472859
0.8553	High Similarity	NPC470607
0.8553	High Similarity	NPC287872
0.8553	High Similarity	NPC74319
0.8545	High Similarity	NPC470438
0.8544	High Similarity	NPC127406
0.8537	High Similarity	NPC105511
0.8537	High Similarity	NPC44558
0.8537	High Similarity	NPC210808
0.8537	High Similarity	NPC199079
0.8537	High Similarity	NPC43434
0.8537	High Similarity	NPC472129
0.8535	High Similarity	NPC194095
0.8535	High Similarity	NPC301233
0.8535	High Similarity	NPC327032
0.8535	High Similarity	NPC191046
0.8526	High Similarity	NPC190217
0.8526	High Similarity	NPC134905
0.8526	High Similarity	NPC289438
0.8526	High Similarity	NPC36130
0.8519	High Similarity	NPC99216
0.8519	High Similarity	NPC72016
0.8516	High Similarity	NPC227980
0.8516	High Similarity	NPC182350
0.8509	High Similarity	NPC278329
0.8509	High Similarity	NPC146837
0.8506	High Similarity	NPC218685
0.8506	High Similarity	NPC23084
0.8503	High Similarity	NPC472387
0.85	High Similarity	NPC166277
0.85	High Similarity	NPC119125
0.85	High Similarity	NPC200708
0.8497	Intermediate Similarity	NPC473867
0.8494	Intermediate Similarity	NPC264735
0.8494	Intermediate Similarity	NPC477848
0.8491	Intermediate Similarity	NPC122809
0.8491	Intermediate Similarity	NPC60966
0.8491	Intermediate Similarity	NPC470606
0.8491	Intermediate Similarity	NPC226759
0.8485	Intermediate Similarity	NPC137871
0.8485	Intermediate Similarity	NPC48773
0.8485	Intermediate Similarity	NPC257011
0.8485	Intermediate Similarity	NPC205076
0.8485	Intermediate Similarity	NPC288152
0.8485	Intermediate Similarity	NPC235575
0.8485	Intermediate Similarity	NPC307518
0.8485	Intermediate Similarity	NPC9002
0.8481	Intermediate Similarity	NPC10205
0.8481	Intermediate Similarity	NPC99233
0.8476	Intermediate Similarity	NPC105025
0.8476	Intermediate Similarity	NPC475942
0.8476	Intermediate Similarity	NPC469931
0.8476	Intermediate Similarity	NPC45638
0.8476	Intermediate Similarity	NPC472133
0.8476	Intermediate Similarity	NPC226294
0.8476	Intermediate Similarity	NPC191653
0.8476	Intermediate Similarity	NPC58053
0.8476	Intermediate Similarity	NPC186807
0.8476	Intermediate Similarity	NPC201292
0.8476	Intermediate Similarity	NPC472381
0.8476	Intermediate Similarity	NPC472383
0.8476	Intermediate Similarity	NPC93337
0.8471	Intermediate Similarity	NPC310661
0.8471	Intermediate Similarity	NPC105827
0.8471	Intermediate Similarity	NPC259767
0.8471	Intermediate Similarity	NPC88484
0.8466	Intermediate Similarity	NPC99957
0.8466	Intermediate Similarity	NPC181616
0.8466	Intermediate Similarity	NPC70441
0.8462	Intermediate Similarity	NPC473966
0.8462	Intermediate Similarity	NPC164527
0.8462	Intermediate Similarity	NPC191154
0.8462	Intermediate Similarity	NPC477240
0.8462	Intermediate Similarity	NPC214454
0.8462	Intermediate Similarity	NPC106025
0.8462	Intermediate Similarity	NPC213382
0.8462	Intermediate Similarity	NPC213723
0.8457	Intermediate Similarity	NPC88043
0.8446	Intermediate Similarity	NPC185778
0.8443	Intermediate Similarity	NPC472384
0.8443	Intermediate Similarity	NPC211532
0.8443	Intermediate Similarity	NPC472992
0.8443	Intermediate Similarity	NPC233994
0.8443	Intermediate Similarity	NPC472385
0.8443	Intermediate Similarity	NPC472991
0.8443	Intermediate Similarity	NPC257714
0.8443	Intermediate Similarity	NPC472380
0.8443	Intermediate Similarity	NPC472382
0.8443	Intermediate Similarity	NPC198324
0.8438	Intermediate Similarity	NPC73511
0.8438	Intermediate Similarity	NPC160780
0.8438	Intermediate Similarity	NPC43761
0.8438	Intermediate Similarity	NPC289811
0.8434	Intermediate Similarity	NPC175230
0.8434	Intermediate Similarity	NPC172033
0.8434	Intermediate Similarity	NPC88560
0.8431	Intermediate Similarity	NPC138915
0.8428	Intermediate Similarity	NPC17521
0.8428	Intermediate Similarity	NPC154341
0.8428	Intermediate Similarity	NPC261866
0.8428	Intermediate Similarity	NPC471405
0.8428	Intermediate Similarity	NPC272550
0.8424	Intermediate Similarity	NPC149011
0.8424	Intermediate Similarity	NPC224462
0.8424	Intermediate Similarity	NPC22195
0.8424	Intermediate Similarity	NPC34287
0.8424	Intermediate Similarity	NPC21190
0.8424	Intermediate Similarity	NPC474434
0.8424	Intermediate Similarity	NPC72249
0.8424	Intermediate Similarity	NPC471416
0.8424	Intermediate Similarity	NPC183357
0.8424	Intermediate Similarity	NPC204937
0.8418	Intermediate Similarity	NPC106625
0.8415	Intermediate Similarity	NPC48640
0.8415	Intermediate Similarity	NPC93099
0.8415	Intermediate Similarity	NPC298847
0.8415	Intermediate Similarity	NPC45618
0.8415	Intermediate Similarity	NPC146792
0.8415	Intermediate Similarity	NPC58716
0.8415	Intermediate Similarity	NPC149244
0.8415	Intermediate Similarity	NPC135345
0.8411	Intermediate Similarity	NPC80098
0.8408	Intermediate Similarity	NPC134819
0.8408	Intermediate Similarity	NPC240768
0.8408	Intermediate Similarity	NPC200773
0.8408	Intermediate Similarity	NPC70016
0.8408	Intermediate Similarity	NPC215921
0.8405	Intermediate Similarity	NPC294722

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 NPC34965 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	267
0.1-0.2	780
0.2-0.3	1847
0.3-0.4	2545
0.4-0.5	2057
0.5-0.6	1117
0.6-0.7	379
0.7-0.8	151
0.8-0.85	7
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8434	Intermediate Similarity	NPD6559	Discontinued
0.8415	Intermediate Similarity	NPD3818	Discontinued
0.8383	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.8375	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.8365	Intermediate Similarity	NPD5402	Approved
0.8144	Intermediate Similarity	NPD7054	Approved
0.8118	Intermediate Similarity	NPD8313	Approved
0.8118	Intermediate Similarity	NPD8312	Approved
0.8117	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.8103	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.8101	Intermediate Similarity	NPD1653	Approved
0.8095	Intermediate Similarity	NPD7074	Phase 3
0.8095	Intermediate Similarity	NPD7472	Approved
0.8067	Intermediate Similarity	NPD447	Suspended
0.8047	Intermediate Similarity	NPD6797	Phase 2
0.8	Intermediate Similarity	NPD7251	Discontinued
0.7974	Intermediate Similarity	NPD2935	Discontinued
0.7953	Intermediate Similarity	NPD7808	Phase 3
0.7929	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7927	Intermediate Similarity	NPD7075	Discontinued
0.7925	Intermediate Similarity	NPD5403	Approved
0.7866	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7866	Intermediate Similarity	NPD3882	Suspended
0.7862	Intermediate Similarity	NPD1091	Approved
0.7857	Intermediate Similarity	NPD1551	Phase 2
0.7853	Intermediate Similarity	NPD2801	Approved
0.7829	Intermediate Similarity	NPD1933	Approved
0.7808	Intermediate Similarity	NPD9717	Approved
0.7799	Intermediate Similarity	NPD5401	Approved
0.7791	Intermediate Similarity	NPD1934	Approved
0.7791	Intermediate Similarity	NPD7685	Pre-registration
0.7778	Intermediate Similarity	NPD4380	Phase 2
0.777	Intermediate Similarity	NPD1203	Approved
0.7744	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7744	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7736	Intermediate Similarity	NPD6799	Approved
0.7733	Intermediate Similarity	NPD6832	Phase 2
0.7712	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7697	Intermediate Similarity	NPD3817	Phase 2
0.7683	Intermediate Similarity	NPD6801	Discontinued
0.7663	Intermediate Similarity	NPD7435	Discontinued
0.7658	Intermediate Similarity	NPD4628	Phase 3
0.7647	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7647	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7647	Intermediate Similarity	NPD6166	Phase 2
0.7636	Intermediate Similarity	NPD7819	Suspended
0.7632	Intermediate Similarity	NPD411	Approved
0.7619	Intermediate Similarity	NPD5494	Approved
0.7596	Intermediate Similarity	NPD6777	Approved
0.7596	Intermediate Similarity	NPD6781	Approved
0.7596	Intermediate Similarity	NPD6776	Approved
0.7596	Intermediate Similarity	NPD6782	Approved
0.7596	Intermediate Similarity	NPD6778	Approved
0.7596	Intermediate Similarity	NPD6779	Approved
0.7596	Intermediate Similarity	NPD6780	Approved
0.7578	Intermediate Similarity	NPD2534	Approved
0.7578	Intermediate Similarity	NPD2532	Approved
0.7578	Intermediate Similarity	NPD2533	Approved
0.7558	Intermediate Similarity	NPD3751	Discontinued
0.7532	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7532	Intermediate Similarity	NPD1549	Phase 2
0.753	Intermediate Similarity	NPD8455	Phase 2
0.7515	Intermediate Similarity	NPD7411	Suspended
0.7514	Intermediate Similarity	NPD6823	Phase 2
0.7514	Intermediate Similarity	NPD5844	Phase 1
0.75	Intermediate Similarity	NPD3226	Approved
0.7486	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7483	Intermediate Similarity	NPD1019	Discontinued
0.7474	Intermediate Similarity	NPD7783	Phase 2
0.7474	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.747	Intermediate Similarity	NPD37	Approved
0.7468	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7468	Intermediate Similarity	NPD7266	Discontinued
0.7468	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7468	Intermediate Similarity	NPD2346	Discontinued
0.7457	Intermediate Similarity	NPD7228	Approved
0.7456	Intermediate Similarity	NPD6234	Discontinued
0.7455	Intermediate Similarity	NPD6599	Discontinued
0.7452	Intermediate Similarity	NPD7033	Discontinued
0.7448	Intermediate Similarity	NPD9493	Approved
0.744	Intermediate Similarity	NPD4967	Phase 2
0.744	Intermediate Similarity	NPD4966	Approved
0.744	Intermediate Similarity	NPD4965	Approved
0.7438	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7429	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7427	Intermediate Similarity	NPD3787	Discontinued
0.7421	Intermediate Similarity	NPD7874	Approved
0.7421	Intermediate Similarity	NPD7875	Clinical (unspecified phase)
0.7416	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7407	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7407	Intermediate Similarity	NPD1511	Approved
0.7403	Intermediate Similarity	NPD2313	Discontinued
0.7396	Intermediate Similarity	NPD3749	Approved
0.7391	Intermediate Similarity	NPD6190	Approved
0.738	Intermediate Similarity	NPD7697	Approved
0.738	Intermediate Similarity	NPD7696	Phase 3
0.738	Intermediate Similarity	NPD7698	Approved
0.7378	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7374	Intermediate Similarity	NPD8434	Phase 2
0.7372	Intermediate Similarity	NPD230	Phase 1
0.7368	Intermediate Similarity	NPD7199	Phase 2
0.7365	Intermediate Similarity	NPD6844	Discontinued
0.7362	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.7362	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7342	Intermediate Similarity	NPD2799	Discontinued
0.734	Intermediate Similarity	NPD7871	Phase 2
0.734	Intermediate Similarity	NPD7870	Phase 2
0.7337	Intermediate Similarity	NPD7768	Phase 2
0.7326	Intermediate Similarity	NPD6232	Discontinued
0.7322	Intermediate Similarity	NPD6534	Approved
0.7322	Intermediate Similarity	NPD6535	Approved
0.7317	Intermediate Similarity	NPD1512	Approved
0.7316	Intermediate Similarity	NPD7701	Phase 2
0.7315	Intermediate Similarity	NPD3496	Discontinued
0.7296	Intermediate Similarity	NPD2796	Approved
0.729	Intermediate Similarity	NPD1699	Clinical (unspecified phase)
0.7289	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7278	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7278	Intermediate Similarity	NPD8150	Discontinued
0.7273	Intermediate Similarity	NPD920	Approved
0.7267	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7256	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7255	Intermediate Similarity	NPD5647	Approved
0.725	Intermediate Similarity	NPD6004	Phase 3
0.725	Intermediate Similarity	NPD6005	Phase 3
0.725	Intermediate Similarity	NPD6003	Clinical (unspecified phase)
0.725	Intermediate Similarity	NPD6006	Clinical (unspecified phase)
0.725	Intermediate Similarity	NPD6002	Phase 3
0.7244	Intermediate Similarity	NPD6233	Phase 2
0.7241	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.7233	Intermediate Similarity	NPD1510	Phase 2
0.7233	Intermediate Similarity	NPD4308	Phase 3
0.7222	Intermediate Similarity	NPD3750	Approved
0.7219	Intermediate Similarity	NPD1465	Phase 2
0.7215	Intermediate Similarity	NPD6653	Approved
0.7205	Intermediate Similarity	NPD2424	Discontinued
0.7204	Intermediate Similarity	NPD7699	Phase 2
0.7204	Intermediate Similarity	NPD7700	Phase 2
0.7202	Intermediate Similarity	NPD7801	Approved
0.72	Intermediate Similarity	NPD7473	Discontinued
0.7197	Intermediate Similarity	NPD1240	Approved
0.7184	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7179	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7174	Intermediate Similarity	NPD6212	Phase 3
0.7174	Intermediate Similarity	NPD6214	Clinical (unspecified phase)
0.7174	Intermediate Similarity	NPD6213	Phase 3
0.7168	Intermediate Similarity	NPD6959	Discontinued
0.7168	Intermediate Similarity	NPD1247	Approved
0.716	Intermediate Similarity	NPD2800	Approved
0.7152	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD6355	Discontinued
0.7151	Intermediate Similarity	NPD919	Approved
0.7143	Intermediate Similarity	NPD2798	Approved
0.7143	Intermediate Similarity	NPD2344	Approved
0.7143	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7133	Intermediate Similarity	NPD1778	Approved
0.7126	Intermediate Similarity	NPD5711	Approved
0.7126	Intermediate Similarity	NPD5710	Approved
0.7114	Intermediate Similarity	NPD9545	Approved
0.7107	Intermediate Similarity	NPD1607	Approved
0.7098	Intermediate Similarity	NPD8151	Discontinued
0.7095	Intermediate Similarity	NPD7240	Approved
0.7092	Intermediate Similarity	NPD7930	Approved
0.7089	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7083	Intermediate Similarity	NPD7584	Approved
0.7078	Intermediate Similarity	NPD2797	Approved
0.707	Intermediate Similarity	NPD6798	Discontinued
0.707	Intermediate Similarity	NPD3764	Approved
0.7068	Intermediate Similarity	NPD8320	Phase 1
0.7068	Intermediate Similarity	NPD8319	Approved
0.7063	Intermediate Similarity	NPD7097	Phase 1
0.7055	Intermediate Similarity	NPD1652	Phase 2
0.7055	Intermediate Similarity	NPD1243	Approved
0.705	Intermediate Similarity	NPD8155	Clinical (unspecified phase)
0.7039	Intermediate Similarity	NPD5953	Discontinued
0.703	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7027	Intermediate Similarity	NPD6671	Approved
0.7013	Intermediate Similarity	NPD3225	Approved
0.6993	Remote Similarity	NPD1608	Approved
0.6989	Remote Similarity	NPD3926	Phase 2
0.6987	Remote Similarity	NPD2861	Phase 2
0.6987	Remote Similarity	NPD9494	Approved
0.6982	Remote Similarity	NPD7458	Discontinued
0.6981	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6981	Remote Similarity	NPD4307	Phase 2
0.6981	Remote Similarity	NPD1613	Approved
0.697	Remote Similarity	NPD2309	Approved
0.6962	Remote Similarity	NPD3268	Approved
0.6959	Remote Similarity	NPD7585	Approved
0.6946	Remote Similarity	NPD4661	Approved
0.6946	Remote Similarity	NPD4662	Approved
0.6937	Remote Similarity	NPD5123	Clinical (unspecified phase)
0.6937	Remote Similarity	NPD5124	Phase 1
0.6933	Remote Similarity	NPD5763	Approved
0.6933	Remote Similarity	NPD5762	Approved
0.6928	Remote Similarity	NPD422	Phase 1
0.6927	Remote Similarity	NPD7286	Phase 2
0.6919	Remote Similarity	NPD5760	Phase 2
0.6919	Remote Similarity	NPD5761	Phase 2

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