NPASS Compound

Structure

CID239961 OpenBabel06191716042D 38 41 0 0 1 0 0 0 0 0999 V2000 -9.3988 1.6285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1667 1.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4375 6.2158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3988 1.6285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3988 1.6285 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 -8.7648 2.9945 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 -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 -6.1667 2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1067 5.4727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8988 4.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0327 2.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.7648 3.9945 0.0000 C 0 0 1 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 -9.1012 5.5772 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 -7.8988 2.4945 0.0000 C 0 0 1 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 -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 -9.6012 6.4432 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 -4.4347 2.4945 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 -9.5079 4.6637 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 5 2 0 0 0 0 2 12 2 0 0 0 0 3 13 1 0 0 0 0 5 25 1 0 0 0 0 6 14 1 0 0 0 0 6 15 1 0 0 0 0 7 25 1 0 0 0 0 8 12 1 0 0 0 0 8 34 1 0 0 0 0 9 35 1 0 0 0 0 10 26 1 0 0 0 0 10 27 1 0 0 0 0 11 26 1 0 0 0 0 11 36 1 0 0 0 0 12 15 1 0 0 0 0 13 14 2 0 0 0 0 13 22 1 0 0 0 0 14 16 1 0 0 0 0 15 25 1 1 0 0 0 16 7 1 6 0 0 0 16 37 1 0 0 0 0 17 9 1 1 0 0 0 17 18 1 0 0 0 0 17 38 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 6 0 0 0 19 20 1 0 0 0 0 19 29 1 1 0 0 0 20 23 1 0 0 0 0 20 30 1 6 0 0 0 21 24 1 0 0 0 0 21 26 1 6 0 0 0 21 31 1 0 0 0 0 22 32 2 0 0 0 0 22 37 1 0 0 0 0 23 34 1 1 0 0 0 23 38 1 0 0 0 0 24 35 1 1 0 0 0 24 36 1 0 0 0 0 25 4 1 1 0 0 0 26 33 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	542.24
Volume:	518.963
LogP:	0.771
LogD:	0.425
LogS:	-2.496
# Rotatable Bonds:	9
TPSA:	191.67
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.189
Synthetic Accessibility Score:	5.637
Fsp3:	0.692
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:	-6.188
MDCK Permeability:	8.165226063283626e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.969
Human Intestinal Absorption (HIA):	0.85
20% Bioavailability (F20%):	0.935
30% Bioavailability (F30%):	0.93

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.094
Plasma Protein Binding (PPB):	73.39562225341797%
Volume Distribution (VD):	0.515
Pgp-substrate:	18.871187210083008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.236
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.103
CYP3A4-inhibitor:	0.05
CYP3A4-substrate:	0.066

ADMET: Excretion

Clearance (CL):	0.84
Half-life (T1/2):	0.817

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.241
Drug-inuced Liver Injury (DILI):	0.774
AMES Toxicity:	0.857
Rat Oral Acute Toxicity:	0.486
Maximum Recommended Daily Dose:	0.141
Skin Sensitization:	0.267
Carcinogencity:	0.459
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.487

Download Data

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

Natural Product: NPC239961

Natural Product ID:	NPC239961
*Common Name:**	Sarcaglaboside D
IUPAC Name:	(5R,6S,7aS)-5-[3-[(2R,3R,4S,5S,6R)-6-[[(2R,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl]oxyprop-1-en-2-yl]-6-ethenyl-3,6-dimethyl-4,5,7,7a-tetrahydro-1-benzofuran-2-one
Synonyms:	sarcaglaboside D
Standard InCHIKey:	NYVXYMLUZXJHAU-LVVJISPMSA-N
Standard InCHI:	InChI=1S/C26H38O12/c1-5-25(4)7-16-14(13(3)22(32)37-16)6-15(25)12(2)8-34-23-20(30)19(29)18(28)17(38-23)9-35-24-21(31)26(33,10-27)11-36-24/h5,15-21,23-24,27-31,33H,1-2,6-11H2,3-4H3/t15-,16-,17+,18+,19-,20+,21-,23+,24+,25+,26+/m0/s1
SMILES:	C=C[C@]1(C)C[C@@H]2OC(=O)C(=C2C[C@H]1C(=C)CO[C@@H]1O[C@H](CO[C@@H]2OC[C@]([C@H]2O)(O)CO)[C@H]([C@@H]([C@H]1O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL514349
PubChem CID:	11497571
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene 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
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	Whole plant	n.a.	n.a.	PMID[16643038]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20038159]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	aerial part	n.a.	n.a.	PMID[25442304]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11301	Ulmus glabra	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11301	Ulmus glabra	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11301	Ulmus glabra	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10577	Loranthus glaber	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9997	Pandanus dubius	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9210	Desmodium uncinatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	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
Others	2

Activity Type	# Activity
NON-MOLECULAR	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	27.0	%	PMID[525024]
NPT27	Others	Unspecified		Activity	=	46.3	%	PMID[525024]

☑ 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 NPC239961 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	189
0.1-0.2	1143
0.2-0.3	4225
0.3-0.4	9122
0.4-0.5	11538
0.5-0.6	7524
0.6-0.7	6059
0.7-0.8	2573
0.8-0.85	285
0.85-0.9	29
0.9-0.95	9
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9588	High Similarity	NPC198992
0.9208	High Similarity	NPC82251
0.91	High Similarity	NPC121423
0.902	High Similarity	NPC85670
0.8942	High Similarity	NPC206618
0.8846	High Similarity	NPC38948
0.8762	High Similarity	NPC257853
0.8725	High Similarity	NPC472815
0.8667	High Similarity	NPC135015
0.8667	High Similarity	NPC48548
0.8667	High Similarity	NPC128795
0.8667	High Similarity	NPC219900
0.8667	High Similarity	NPC217921
0.8667	High Similarity	NPC392
0.8667	High Similarity	NPC177524
0.8654	High Similarity	NPC218158
0.8641	High Similarity	NPC120009
0.8624	High Similarity	NPC99620
0.8624	High Similarity	NPC193382
0.8624	High Similarity	NPC199428
0.8624	High Similarity	NPC5311
0.8624	High Similarity	NPC310341
0.8611	High Similarity	NPC264153
0.8585	High Similarity	NPC316974
0.8585	High Similarity	NPC40728
0.8571	High Similarity	NPC125423
0.8571	High Similarity	NPC88013
0.8545	High Similarity	NPC309034
0.8545	High Similarity	NPC93883
0.8545	High Similarity	NPC34390
0.8545	High Similarity	NPC474418
0.8545	High Similarity	NPC471355
0.8545	High Similarity	NPC471351
0.8545	High Similarity	NPC471354
0.8545	High Similarity	NPC84987
0.8545	High Similarity	NPC244402
0.8545	High Similarity	NPC77319
0.8545	High Similarity	NPC99728
0.8545	High Similarity	NPC142066
0.8545	High Similarity	NPC50305
0.8545	High Similarity	NPC152615
0.8545	High Similarity	NPC157376
0.8545	High Similarity	NPC203862
0.8545	High Similarity	NPC158344
0.8545	High Similarity	NPC471353
0.8545	High Similarity	NPC473852
0.8545	High Similarity	NPC27507
0.8545	High Similarity	NPC243196
0.8545	High Similarity	NPC87250
0.8545	High Similarity	NPC196429
0.8544	High Similarity	NPC201191
0.8544	High Similarity	NPC150463
0.8532	High Similarity	NPC471633
0.8532	High Similarity	NPC31354
0.8532	High Similarity	NPC84949
0.8532	High Similarity	NPC69576
0.8519	High Similarity	NPC328074
0.8519	High Similarity	NPC321272
0.8519	High Similarity	NPC470025
0.8519	High Similarity	NPC317460
0.8515	High Similarity	NPC96597
0.8515	High Similarity	NPC309503
0.8515	High Similarity	NPC125551
0.8515	High Similarity	NPC91197
0.8515	High Similarity	NPC239547
0.8515	High Similarity	NPC155319
0.8505	High Similarity	NPC316708
0.8491	Intermediate Similarity	NPC311223
0.8468	Intermediate Similarity	NPC83287
0.8462	Intermediate Similarity	NPC475889
0.8462	Intermediate Similarity	NPC127933
0.8462	Intermediate Similarity	NPC7644
0.8462	Intermediate Similarity	NPC7613
0.8462	Intermediate Similarity	NPC281378
0.8447	Intermediate Similarity	NPC280991
0.8447	Intermediate Similarity	NPC11974
0.844	Intermediate Similarity	NPC470027
0.8426	Intermediate Similarity	NPC470026
0.8426	Intermediate Similarity	NPC17791
0.8396	Intermediate Similarity	NPC475074
0.8396	Intermediate Similarity	NPC109376
0.8393	Intermediate Similarity	NPC469756
0.8393	Intermediate Similarity	NPC30483
0.8393	Intermediate Similarity	NPC29639
0.8393	Intermediate Similarity	NPC32177
0.8393	Intermediate Similarity	NPC292467
0.8393	Intermediate Similarity	NPC55532
0.8393	Intermediate Similarity	NPC44899
0.8393	Intermediate Similarity	NPC470897
0.8393	Intermediate Similarity	NPC329905
0.8393	Intermediate Similarity	NPC236973
0.8393	Intermediate Similarity	NPC5883
0.8393	Intermediate Similarity	NPC304260
0.8381	Intermediate Similarity	NPC470321
0.8381	Intermediate Similarity	NPC473207
0.8381	Intermediate Similarity	NPC264867
0.8381	Intermediate Similarity	NPC81567
0.8381	Intermediate Similarity	NPC201880
0.8378	Intermediate Similarity	NPC474483
0.8378	Intermediate Similarity	NPC290693
0.8365	Intermediate Similarity	NPC238397
0.8365	Intermediate Similarity	NPC471363
0.8365	Intermediate Similarity	NPC472552
0.835	Intermediate Similarity	NPC324841
0.8349	Intermediate Similarity	NPC473125
0.8333	Intermediate Similarity	NPC177047
0.8333	Intermediate Similarity	NPC471082
0.8333	Intermediate Similarity	NPC205143
0.8333	Intermediate Similarity	NPC119550
0.8319	Intermediate Similarity	NPC475629
0.8319	Intermediate Similarity	NPC470312
0.8319	Intermediate Similarity	NPC475556
0.8319	Intermediate Similarity	NPC474466
0.8319	Intermediate Similarity	NPC475136
0.8319	Intermediate Similarity	NPC72260
0.8318	Intermediate Similarity	NPC224660
0.8318	Intermediate Similarity	NPC470024
0.8304	Intermediate Similarity	NPC218093
0.8302	Intermediate Similarity	NPC51719
0.8302	Intermediate Similarity	NPC172867
0.83	Intermediate Similarity	NPC474835
0.8288	Intermediate Similarity	NPC471816
0.8286	Intermediate Similarity	NPC134270
0.8286	Intermediate Similarity	NPC473070
0.8283	Intermediate Similarity	NPC202886
0.8273	Intermediate Similarity	NPC474410
0.8273	Intermediate Similarity	NPC473159
0.8273	Intermediate Similarity	NPC49413
0.8273	Intermediate Similarity	NPC40133
0.8273	Intermediate Similarity	NPC44298
0.8273	Intermediate Similarity	NPC473128
0.8273	Intermediate Similarity	NPC293658
0.8273	Intermediate Similarity	NPC290608
0.8269	Intermediate Similarity	NPC472554
0.8269	Intermediate Similarity	NPC477717
0.8261	Intermediate Similarity	NPC27363
0.8246	Intermediate Similarity	NPC475590
0.8246	Intermediate Similarity	NPC475419
0.8246	Intermediate Similarity	NPC474908
0.8246	Intermediate Similarity	NPC314535
0.8246	Intermediate Similarity	NPC231518
0.8246	Intermediate Similarity	NPC40749
0.8246	Intermediate Similarity	NPC173555
0.8246	Intermediate Similarity	NPC475219
0.8246	Intermediate Similarity	NPC120390
0.823	Intermediate Similarity	NPC470914
0.823	Intermediate Similarity	NPC153085
0.823	Intermediate Similarity	NPC268326
0.823	Intermediate Similarity	NPC291820
0.823	Intermediate Similarity	NPC81222
0.8224	Intermediate Similarity	NPC184512
0.8224	Intermediate Similarity	NPC471205
0.8224	Intermediate Similarity	NPC122816
0.8218	Intermediate Similarity	NPC256368
0.8208	Intermediate Similarity	NPC473068
0.82	Intermediate Similarity	NPC477749
0.8198	Intermediate Similarity	NPC106446
0.819	Intermediate Similarity	NPC470571
0.819	Intermediate Similarity	NPC214277
0.8182	Intermediate Similarity	NPC477748
0.8174	Intermediate Similarity	NPC474423
0.8174	Intermediate Similarity	NPC115349
0.8174	Intermediate Similarity	NPC264336
0.8174	Intermediate Similarity	NPC193893
0.8174	Intermediate Similarity	NPC74259
0.8173	Intermediate Similarity	NPC38855
0.8173	Intermediate Similarity	NPC477721
0.8173	Intermediate Similarity	NPC477716
0.8173	Intermediate Similarity	NPC130792
0.8165	Intermediate Similarity	NPC170974
0.8165	Intermediate Similarity	NPC103627
0.8165	Intermediate Similarity	NPC191439
0.8158	Intermediate Similarity	NPC107607
0.8158	Intermediate Similarity	NPC48692
0.8158	Intermediate Similarity	NPC476150
0.8158	Intermediate Similarity	NPC135369
0.8158	Intermediate Similarity	NPC476127
0.8148	Intermediate Similarity	NPC181994
0.8148	Intermediate Similarity	NPC473069
0.8142	Intermediate Similarity	NPC473828
0.8142	Intermediate Similarity	NPC473617
0.8131	Intermediate Similarity	NPC470767
0.8131	Intermediate Similarity	NPC470763
0.8131	Intermediate Similarity	NPC252296
0.8125	Intermediate Similarity	NPC207637
0.812	Intermediate Similarity	NPC250556
0.812	Intermediate Similarity	NPC469750
0.8119	Intermediate Similarity	NPC472196
0.8119	Intermediate Similarity	NPC91654
0.8119	Intermediate Similarity	NPC67398
0.8119	Intermediate Similarity	NPC156553
0.8119	Intermediate Similarity	NPC474792
0.8119	Intermediate Similarity	NPC238090
0.8119	Intermediate Similarity	NPC472195
0.8113	Intermediate Similarity	NPC23584
0.8108	Intermediate Similarity	NPC311592
0.8108	Intermediate Similarity	NPC75167
0.8108	Intermediate Similarity	NPC287075
0.8103	Intermediate Similarity	NPC117445
0.8103	Intermediate Similarity	NPC308262

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 NPC239961 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	159
0.1-0.2	1324
0.2-0.3	3911
0.3-0.4	2467
0.4-0.5	782
0.5-0.6	271
0.6-0.7	197
0.7-0.8	26
0.8-0.85	13
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8667	High Similarity	NPD6686	Approved
0.8468	Intermediate Similarity	NPD7327	Approved
0.8468	Intermediate Similarity	NPD7328	Approved
0.8393	Intermediate Similarity	NPD7516	Approved
0.8319	Intermediate Similarity	NPD8377	Approved
0.8319	Intermediate Similarity	NPD8294	Approved
0.8246	Intermediate Similarity	NPD8033	Approved
0.8246	Intermediate Similarity	NPD8335	Approved
0.8246	Intermediate Similarity	NPD8380	Approved
0.8246	Intermediate Similarity	NPD8379	Approved
0.8246	Intermediate Similarity	NPD8296	Approved
0.8246	Intermediate Similarity	NPD8378	Approved
0.812	Intermediate Similarity	NPD7507	Approved
0.7931	Intermediate Similarity	NPD7503	Approved
0.7917	Intermediate Similarity	NPD7319	Approved
0.7593	Intermediate Similarity	NPD5344	Discontinued
0.757	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.757	Intermediate Similarity	NPD4225	Approved
0.7478	Intermediate Similarity	NPD8133	Approved
0.7411	Intermediate Similarity	NPD6412	Phase 2
0.7407	Intermediate Similarity	NPD7638	Approved
0.7404	Intermediate Similarity	NPD7838	Discovery
0.7404	Intermediate Similarity	NPD6698	Approved
0.7404	Intermediate Similarity	NPD46	Approved
0.7339	Intermediate Similarity	NPD7640	Approved
0.7339	Intermediate Similarity	NPD7639	Approved
0.7333	Intermediate Similarity	NPD8515	Approved
0.7333	Intermediate Similarity	NPD8517	Approved
0.7333	Intermediate Similarity	NPD8513	Phase 3
0.7333	Intermediate Similarity	NPD8516	Approved
0.7327	Intermediate Similarity	NPD6400	Clinical (unspecified phase)
0.7304	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7281	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7182	Intermediate Similarity	NPD6648	Approved
0.7131	Intermediate Similarity	NPD6370	Approved
0.713	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.712	Intermediate Similarity	NPD7736	Approved
0.7073	Intermediate Similarity	NPD8328	Phase 3
0.7069	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.704	Intermediate Similarity	NPD8293	Discontinued
0.7016	Intermediate Similarity	NPD7492	Approved
0.6967	Remote Similarity	NPD6054	Approved
0.696	Remote Similarity	NPD6616	Approved
0.6957	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6905	Remote Similarity	NPD7078	Approved
0.686	Remote Similarity	NPD7115	Discovery
0.6829	Remote Similarity	NPD6059	Approved
0.681	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6807	Remote Similarity	NPD6882	Approved
0.678	Remote Similarity	NPD6371	Approved
0.6774	Remote Similarity	NPD6015	Approved
0.6774	Remote Similarity	NPD6016	Approved
0.6772	Remote Similarity	NPD8074	Phase 3
0.6754	Remote Similarity	NPD7632	Discontinued
0.6752	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.6739	Remote Similarity	NPD7625	Phase 1
0.6721	Remote Similarity	NPD6009	Approved
0.6721	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.672	Remote Similarity	NPD5988	Approved
0.6697	Remote Similarity	NPD7637	Suspended
0.6694	Remote Similarity	NPD6319	Approved
0.6667	Remote Similarity	NPD8297	Approved
0.6667	Remote Similarity	NPD6067	Discontinued
0.6636	Remote Similarity	NPD7524	Approved
0.6635	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6612	Remote Similarity	NPD4632	Approved
0.6577	Remote Similarity	NPD5282	Discontinued
0.6567	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.6545	Remote Similarity	NPD7983	Approved
0.6535	Remote Similarity	NPD7829	Approved
0.6535	Remote Similarity	NPD7830	Approved
0.6529	Remote Similarity	NPD6053	Discontinued
0.6518	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6509	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD5778	Approved
0.6486	Remote Similarity	NPD5779	Approved
0.6481	Remote Similarity	NPD4250	Approved
0.6481	Remote Similarity	NPD4251	Approved
0.6471	Remote Similarity	NPD6899	Approved
0.6471	Remote Similarity	NPD7320	Approved
0.6471	Remote Similarity	NPD6881	Approved
0.6449	Remote Similarity	NPD1694	Approved
0.6446	Remote Similarity	NPD6649	Approved
0.6446	Remote Similarity	NPD6650	Approved
0.6441	Remote Similarity	NPD6675	Approved
0.6441	Remote Similarity	NPD7128	Approved
0.6441	Remote Similarity	NPD6402	Approved
0.6441	Remote Similarity	NPD5739	Approved
0.6434	Remote Similarity	NPD8451	Approved
0.6417	Remote Similarity	NPD6373	Approved
0.6417	Remote Similarity	NPD6372	Approved
0.6415	Remote Similarity	NPD6695	Phase 3
0.6406	Remote Similarity	NPD7642	Approved
0.6396	Remote Similarity	NPD6411	Approved
0.6389	Remote Similarity	NPD4249	Approved
0.6387	Remote Similarity	NPD5697	Approved
0.6385	Remote Similarity	NPD8448	Approved
0.6364	Remote Similarity	NPD7102	Approved
0.6364	Remote Similarity	NPD7290	Approved
0.6364	Remote Similarity	NPD6883	Approved
0.6339	Remote Similarity	NPD8171	Discontinued
0.6336	Remote Similarity	NPD6033	Approved
0.6311	Remote Similarity	NPD6617	Approved
0.6311	Remote Similarity	NPD8130	Phase 1
0.6311	Remote Similarity	NPD6847	Approved
0.6311	Remote Similarity	NPD6869	Approved
0.6303	Remote Similarity	NPD6008	Approved
0.6296	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6283	Remote Similarity	NPD7748	Approved
0.6281	Remote Similarity	NPD6014	Approved
0.6281	Remote Similarity	NPD6013	Approved
0.6281	Remote Similarity	NPD6012	Approved
0.6279	Remote Similarity	NPD7604	Phase 2
0.627	Remote Similarity	NPD7641	Discontinued
0.6261	Remote Similarity	NPD6083	Phase 2
0.6261	Remote Similarity	NPD7902	Approved
0.6261	Remote Similarity	NPD6084	Phase 2
0.625	Remote Similarity	NPD7515	Phase 2
0.625	Remote Similarity	NPD5701	Approved
0.625	Remote Similarity	NPD8444	Approved
0.625	Remote Similarity	NPD6921	Approved
0.625	Remote Similarity	NPD5983	Phase 2
0.6241	Remote Similarity	NPD8391	Approved
0.6241	Remote Similarity	NPD8392	Approved
0.6241	Remote Similarity	NPD8390	Approved
0.6231	Remote Similarity	NPD8342	Approved
0.6231	Remote Similarity	NPD8341	Approved
0.6231	Remote Similarity	NPD8299	Approved
0.6231	Remote Similarity	NPD8340	Approved
0.6218	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.6216	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6216	Remote Similarity	NPD6051	Approved
0.6216	Remote Similarity	NPD6101	Approved
0.6202	Remote Similarity	NPD8080	Discontinued
0.6198	Remote Similarity	NPD6011	Approved
0.6195	Remote Similarity	NPD6399	Phase 3
0.619	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.619	Remote Similarity	NPD7505	Discontinued
0.6183	Remote Similarity	NPD6336	Discontinued
0.6182	Remote Similarity	NPD7750	Discontinued
0.6174	Remote Similarity	NPD7839	Suspended
0.6161	Remote Similarity	NPD5785	Approved
0.6161	Remote Similarity	NPD3168	Discontinued
0.6132	Remote Similarity	NPD4822	Approved
0.6132	Remote Similarity	NPD4819	Approved
0.6132	Remote Similarity	NPD6931	Approved
0.6132	Remote Similarity	NPD4820	Approved
0.6132	Remote Similarity	NPD7332	Phase 2
0.6132	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6132	Remote Similarity	NPD6930	Phase 2
0.6132	Remote Similarity	NPD7514	Phase 3
0.6132	Remote Similarity	NPD4821	Approved
0.6132	Remote Similarity	NPD7525	Registered
0.6119	Remote Similarity	NPD5956	Approved
0.6111	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6111	Remote Similarity	NPD3669	Approved
0.6098	Remote Similarity	NPD4634	Approved
0.6087	Remote Similarity	NPD5695	Phase 3
0.6074	Remote Similarity	NPD7260	Phase 2
0.6071	Remote Similarity	NPD1695	Approved
0.6058	Remote Similarity	NPD6933	Approved
0.605	Remote Similarity	NPD5211	Phase 2
0.6048	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.604	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6038	Remote Similarity	NPD6929	Approved
0.6034	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.6029	Remote Similarity	NPD8449	Approved
0.6029	Remote Similarity	NPD8338	Approved
0.6017	Remote Similarity	NPD4696	Approved
0.6017	Remote Similarity	NPD5285	Approved
0.6017	Remote Similarity	NPD5286	Approved
0.6	Remote Similarity	NPD6932	Approved
0.6	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6	Remote Similarity	NPD7900	Approved
0.6	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.6	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.5985	Remote Similarity	NPD8450	Suspended
0.5983	Remote Similarity	NPD4755	Approved
0.5982	Remote Similarity	NPD6903	Approved
0.5969	Remote Similarity	NPD7100	Approved
0.5969	Remote Similarity	NPD7101	Approved
0.5965	Remote Similarity	NPD7087	Discontinued
0.5965	Remote Similarity	NPD6079	Approved
0.5963	Remote Similarity	NPD5362	Discontinued
0.5963	Remote Similarity	NPD7154	Phase 3
0.5954	Remote Similarity	NPD5126	Approved
0.5954	Remote Similarity	NPD5125	Phase 3
0.595	Remote Similarity	NPD5141	Approved
0.5948	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.5946	Remote Similarity	NPD3618	Phase 1
0.5946	Remote Similarity	NPD7334	Approved
0.5946	Remote Similarity	NPD6684	Approved
0.5946	Remote Similarity	NPD5330	Approved
0.5946	Remote Similarity	NPD7521	Approved
0.5946	Remote Similarity	NPD6409	Approved
0.5946	Remote Similarity	NPD7146	Approved
0.5944	Remote Similarity	NPD7266	Discontinued
0.5943	Remote Similarity	NPD4268	Approved
0.5943	Remote Similarity	NPD7145	Approved
0.5943	Remote Similarity	NPD5784	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