NPASS Compound

Structure

NPC25889 OpenBabel07101718222D 47 51 0 0 1 0 0 0 0 0999 V2000 4.7321 4.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7321 0.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7321 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1340 0.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1340 -0.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7321 -0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8660 -2.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 2.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 4.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3301 -0.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8660 3.7679 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0000 1.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8660 2.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3301 0.7679 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0000 -0.7321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8660 0.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1962 1.2679 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5000 -0.8660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7321 1.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1962 2.2679 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0000 -1.7321 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3301 2.7679 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.7321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7321 2.2679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4641 2.2679 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5000 -0.8660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0000 -1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8660 -0.2321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0000 -1.7321 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0000 5.2679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1962 -0.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 1.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0622 0.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5000 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5981 0.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0622 2.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3301 3.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4641 1.2679 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 5.5981 2.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4 7 1 0 0 0 0 4 8 1 0 0 0 0 5 6 1 0 0 0 0 5 14 1 0 0 0 0 6 18 1 0 0 0 0 7 31 1 0 0 0 0 8 32 1 0 0 0 0 9 14 2 0 0 0 0 9 15 1 0 0 0 0 10 13 1 0 0 0 0 10 33 1 0 0 0 0 11 34 1 0 0 0 0 12 35 1 0 0 0 0 13 1 1 1 0 0 0 13 15 1 0 0 0 0 14 19 1 0 0 0 0 15 27 2 0 0 0 0 16 11 1 1 0 0 0 16 20 1 0 0 0 0 16 44 1 0 0 0 0 17 12 1 1 0 0 0 17 21 1 0 0 0 0 17 45 1 0 0 0 0 18 31 1 6 0 0 0 18 32 1 0 0 0 0 19 22 2 0 0 0 0 19 31 1 0 0 0 0 20 23 1 0 0 0 0 20 36 1 6 0 0 0 21 24 1 0 0 0 0 21 37 1 6 0 0 0 22 27 1 0 0 0 0 22 38 1 0 0 0 0 23 25 1 0 0 0 0 23 39 1 1 0 0 0 24 26 1 0 0 0 0 24 40 1 1 0 0 0 25 28 1 0 0 0 0 25 41 1 6 0 0 0 26 29 1 0 0 0 0 26 42 1 6 0 0 0 27 46 1 0 0 0 0 28 44 1 0 0 0 0 28 46 1 1 0 0 0 29 45 1 0 0 0 0 29 47 1 1 0 0 0 30 32 1 0 0 0 0 30 43 2 0 0 0 0 30 47 1 0 0 0 0 31 2 1 6 0 0 0 32 3 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	672.3
Volume:	640.553
LogP:	-0.456
LogD:	-0.235
LogS:	-3.021
# Rotatable Bonds:	9
TPSA:	256.29
# H-Bond Aceptor:	15
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.134
Synthetic Accessibility Score:	5.41
Fsp3:	0.781
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.542
MDCK Permeability:	6.924900662852451e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.95
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.188
Plasma Protein Binding (PPB):	52.257789611816406%
Volume Distribution (VD):	0.319
Pgp-substrate:	18.66290855407715%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.213
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.511
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.078
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.089
CYP3A4-inhibitor:	0.014
CYP3A4-substrate:	0.009

ADMET: Excretion

Clearance (CL):	1.162
Half-life (T1/2):	0.669

ADMET: Toxicity

hERG Blockers:	0.169
Human Hepatotoxicity (H-HT):	0.259
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.107
Rat Oral Acute Toxicity:	0.027
Maximum Recommended Daily Dose:	0.029
Skin Sensitization:	0.172
Carcinogencity:	0.042
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.015

Download Data

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

Natural Product: NPC25889

Natural Product ID:	NPC25889
*Common Name:**	[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl] (1S,4As,10Ar)-5-Hydroxy-7-[(2S)-1-Hydroxypropan-2-Yl]-1,4A-Dimethyl-6-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxy-2,3,4,9,10,10A-Hexahydrophenanthrene-1-Carboxylate
IUPAC Name:	[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (1S,4aS,10aR)-5-hydroxy-7-[(2S)-1-hydroxypropan-2-yl]-1,4a-dimethyl-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,3,4,9,10,10a-hexahydrophenanthrene-1-carboxylate
Synonyms:
Standard InCHIKey:	KJRLDWGHZUUHJO-BDONCRHMSA-N
Standard InCHI:	InChI=1S/C32H48O15/c1-13(10-33)15-9-14-5-6-18-31(2,19(14)22(38)27(15)46-28-25(41)23(39)20(36)16(11-34)44-28)7-4-8-32(18,3)30(43)47-29-26(42)24(40)21(37)17(12-35)45-29/h9,13,16-18,20-21,23-26,28-29,33-42H,4-8,10-12H2,1-3H3/t13-,16-,17-,18-,20-,21-,23+,24+,25-,26-,28+,29+,31+,32+/m1/s1
SMILES:	OC[C@H]1O[C@@H](OC(=O)[C@@]2(C)CCC[C@]3([C@H]2CCc2c3c(O)c(c(c2)[C@@H](CO)C)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)C)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL448745
PubChem CID:	24879400
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001755] Diterpene 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
NPO20879	Clerodendrum bungei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18348535]
NPO20879	Clerodendrum bungei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20879	Clerodendrum bungei	Species	Lamiaceae	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	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2511	Cell Line	HGC-27	Homo sapiens	IC50	>	10000.0	nM	PMID[575407]
NPT71	Cell Line	HEK293	Homo sapiens	IC50	>	10000.0	nM	PMID[575407]
NPT319	Cell Line	B16	Mus musculus	IC50	>	10000.0	nM	PMID[575407]

☑ 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 NPC25889 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	382
0.1-0.2	1508
0.2-0.3	3192
0.3-0.4	6389
0.4-0.5	9078
0.5-0.6	7967
0.6-0.7	8822
0.7-0.8	4959
0.8-0.85	341
0.85-0.9	50
0.9-0.95	7
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9416	High Similarity	NPC106669
0.9416	High Similarity	NPC200645
0.9416	High Similarity	NPC475227
0.9221	High Similarity	NPC183380
0.9156	High Similarity	NPC474893
0.9156	High Similarity	NPC475940
0.9156	High Similarity	NPC220006
0.9156	High Similarity	NPC181452
0.9091	High Similarity	NPC290902
0.9091	High Similarity	NPC117788
0.9091	High Similarity	NPC159697
0.9091	High Similarity	NPC474856
0.9091	High Similarity	NPC291326
0.9091	High Similarity	NPC130959
0.9091	High Similarity	NPC474834
0.9091	High Similarity	NPC474795
0.9091	High Similarity	NPC474940
0.9091	High Similarity	NPC303013
0.8982	High Similarity	NPC475054
0.8916	High Similarity	NPC469775
0.8916	High Similarity	NPC100925
0.8916	High Similarity	NPC469773
0.8916	High Similarity	NPC469777
0.8916	High Similarity	NPC295941
0.8916	High Similarity	NPC469776
0.8916	High Similarity	NPC469772
0.8916	High Similarity	NPC32723
0.8916	High Similarity	NPC469774
0.8916	High Similarity	NPC469778
0.8916	High Similarity	NPC135334
0.8855	High Similarity	NPC179240
0.8848	High Similarity	NPC185498
0.8846	High Similarity	NPC179809
0.8831	High Similarity	NPC133251
0.8831	High Similarity	NPC164183
0.8743	High Similarity	NPC52598
0.8727	High Similarity	NPC222531
0.8688	High Similarity	NPC61604
0.8688	High Similarity	NPC245615
0.8688	High Similarity	NPC299706
0.8688	High Similarity	NPC115466
0.8675	High Similarity	NPC306475
0.8671	High Similarity	NPC44452
0.8667	High Similarity	NPC14294
0.8667	High Similarity	NPC116759
0.8655	High Similarity	NPC275690
0.8655	High Similarity	NPC161609
0.865	High Similarity	NPC478269
0.8642	High Similarity	NPC228357
0.8639	High Similarity	NPC316539
0.8608	High Similarity	NPC127046
0.8608	High Similarity	NPC116229
0.8608	High Similarity	NPC470757
0.8588	High Similarity	NPC473630
0.8588	High Similarity	NPC193377
0.8545	High Similarity	NPC478267
0.8545	High Similarity	NPC109061
0.8545	High Similarity	NPC100465
0.8545	High Similarity	NPC152424
0.8545	High Similarity	NPC115624
0.8544	High Similarity	NPC58752
0.8544	High Similarity	NPC474991
0.8535	High Similarity	NPC272619
0.8535	High Similarity	NPC286245
0.8528	High Similarity	NPC163635
0.8512	High Similarity	NPC298847
0.8506	High Similarity	NPC167045
0.8506	High Similarity	NPC114120
0.85	High Similarity	NPC145979
0.85	High Similarity	NPC218041
0.85	High Similarity	NPC9933
0.85	High Similarity	NPC214326
0.85	High Similarity	NPC158635
0.85	High Similarity	NPC225815
0.85	High Similarity	NPC185955
0.85	High Similarity	NPC260781
0.85	High Similarity	NPC469707
0.85	High Similarity	NPC229882
0.85	High Similarity	NPC469706
0.85	High Similarity	NPC182368
0.8494	Intermediate Similarity	NPC140346
0.8488	Intermediate Similarity	NPC47191
0.8485	Intermediate Similarity	NPC150943
0.8485	Intermediate Similarity	NPC91634
0.8485	Intermediate Similarity	NPC268718
0.8481	Intermediate Similarity	NPC84786
0.8476	Intermediate Similarity	NPC471878
0.8471	Intermediate Similarity	NPC471922
0.8471	Intermediate Similarity	NPC114550
0.8471	Intermediate Similarity	NPC253015
0.8471	Intermediate Similarity	NPC471921
0.8471	Intermediate Similarity	NPC474075
0.8471	Intermediate Similarity	NPC471065
0.8471	Intermediate Similarity	NPC292712
0.8471	Intermediate Similarity	NPC471920
0.8471	Intermediate Similarity	NPC129930
0.8471	Intermediate Similarity	NPC312006
0.8471	Intermediate Similarity	NPC20114
0.8462	Intermediate Similarity	NPC471870
0.8448	Intermediate Similarity	NPC476203
0.8434	Intermediate Similarity	NPC177100
0.8434	Intermediate Similarity	NPC124747
0.8434	Intermediate Similarity	NPC155754
0.8434	Intermediate Similarity	NPC139540
0.843	Intermediate Similarity	NPC469397
0.843	Intermediate Similarity	NPC79736
0.843	Intermediate Similarity	NPC67629
0.8428	Intermediate Similarity	NPC224674
0.8428	Intermediate Similarity	NPC15956
0.8428	Intermediate Similarity	NPC193473
0.8428	Intermediate Similarity	NPC114505
0.8428	Intermediate Similarity	NPC275284
0.8428	Intermediate Similarity	NPC213074
0.8428	Intermediate Similarity	NPC31325
0.8424	Intermediate Similarity	NPC166456
0.8424	Intermediate Similarity	NPC94220
0.8424	Intermediate Similarity	NPC24339
0.8424	Intermediate Similarity	NPC98083
0.8424	Intermediate Similarity	NPC7543
0.8421	Intermediate Similarity	NPC199357
0.8421	Intermediate Similarity	NPC471871
0.8415	Intermediate Similarity	NPC165483
0.8415	Intermediate Similarity	NPC478055
0.8412	Intermediate Similarity	NPC304125
0.8412	Intermediate Similarity	NPC265563
0.8409	Intermediate Similarity	NPC286301
0.8409	Intermediate Similarity	NPC313063
0.8402	Intermediate Similarity	NPC286809
0.8395	Intermediate Similarity	NPC475579
0.8395	Intermediate Similarity	NPC473773
0.8395	Intermediate Similarity	NPC21902
0.8395	Intermediate Similarity	NPC476452
0.8395	Intermediate Similarity	NPC474442
0.8382	Intermediate Similarity	NPC35266
0.8382	Intermediate Similarity	NPC267549
0.838	Intermediate Similarity	NPC476358
0.8377	Intermediate Similarity	NPC68292
0.8375	Intermediate Similarity	NPC95990
0.8373	Intermediate Similarity	NPC119910
0.8372	Intermediate Similarity	NPC63105
0.8364	Intermediate Similarity	NPC19947
0.8364	Intermediate Similarity	NPC181168
0.8364	Intermediate Similarity	NPC207584
0.8364	Intermediate Similarity	NPC115281
0.8364	Intermediate Similarity	NPC163527
0.8363	Intermediate Similarity	NPC473697
0.8362	Intermediate Similarity	NPC205721
0.8354	Intermediate Similarity	NPC131532
0.8354	Intermediate Similarity	NPC38699
0.8352	Intermediate Similarity	NPC475352
0.8352	Intermediate Similarity	NPC475220
0.8352	Intermediate Similarity	NPC229817
0.8352	Intermediate Similarity	NPC473686
0.8352	Intermediate Similarity	NPC221140
0.8344	Intermediate Similarity	NPC65591
0.8344	Intermediate Similarity	NPC245948
0.8344	Intermediate Similarity	NPC178574
0.8343	Intermediate Similarity	NPC475662
0.8343	Intermediate Similarity	NPC473631
0.8343	Intermediate Similarity	NPC9309
0.8343	Intermediate Similarity	NPC473717
0.8343	Intermediate Similarity	NPC293227
0.8333	Intermediate Similarity	NPC118033
0.8333	Intermediate Similarity	NPC121290
0.8333	Intermediate Similarity	NPC100420
0.8333	Intermediate Similarity	NPC212290
0.8324	Intermediate Similarity	NPC297574
0.8324	Intermediate Similarity	NPC92403
0.8324	Intermediate Similarity	NPC170018
0.8324	Intermediate Similarity	NPC66820
0.8324	Intermediate Similarity	NPC76112
0.8323	Intermediate Similarity	NPC471852
0.8314	Intermediate Similarity	NPC219600
0.8314	Intermediate Similarity	NPC166674
0.8314	Intermediate Similarity	NPC263119
0.8314	Intermediate Similarity	NPC46640
0.8314	Intermediate Similarity	NPC34436
0.8313	Intermediate Similarity	NPC191899
0.8313	Intermediate Similarity	NPC173726
0.8313	Intermediate Similarity	NPC241600
0.8313	Intermediate Similarity	NPC246229
0.8305	Intermediate Similarity	NPC105591
0.8304	Intermediate Similarity	NPC298778
0.8303	Intermediate Similarity	NPC32373
0.8303	Intermediate Similarity	NPC11411
0.8303	Intermediate Similarity	NPC237946
0.8302	Intermediate Similarity	NPC43508
0.8302	Intermediate Similarity	NPC476301
0.8294	Intermediate Similarity	NPC475453
0.8294	Intermediate Similarity	NPC473531
0.8293	Intermediate Similarity	NPC62051
0.8291	Intermediate Similarity	NPC113680
0.8291	Intermediate Similarity	NPC278961
0.8286	Intermediate Similarity	NPC188217
0.8286	Intermediate Similarity	NPC208797
0.8286	Intermediate Similarity	NPC53680
0.8286	Intermediate Similarity	NPC475161
0.8286	Intermediate Similarity	NPC477860
0.8284	Intermediate Similarity	NPC99216
0.8284	Intermediate Similarity	NPC178281

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 NPC25889 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	320
0.1-0.2	923
0.2-0.3	1842
0.3-0.4	2621
0.4-0.5	1946
0.5-0.6	997
0.6-0.7	398
0.7-0.8	95
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8848	High Similarity	NPD7228	Approved
0.8636	High Similarity	NPD6674	Discontinued
0.8424	Intermediate Similarity	NPD6234	Discontinued
0.8405	Intermediate Similarity	NPD8455	Phase 2
0.8344	Intermediate Similarity	NPD37	Approved
0.8324	Intermediate Similarity	NPD8312	Approved
0.8324	Intermediate Similarity	NPD8313	Approved
0.8314	Intermediate Similarity	NPD7240	Approved
0.8303	Intermediate Similarity	NPD4967	Phase 2
0.8303	Intermediate Similarity	NPD4965	Approved
0.8303	Intermediate Similarity	NPD4966	Approved
0.8092	Intermediate Similarity	NPD7074	Phase 3
0.8035	Intermediate Similarity	NPD7054	Approved
0.8	Intermediate Similarity	NPD8127	Discontinued
0.8	Intermediate Similarity	NPD7199	Phase 2
0.7989	Intermediate Similarity	NPD7472	Approved
0.7989	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7935	Intermediate Similarity	NPD7237	Clinical (unspecified phase)
0.7931	Intermediate Similarity	NPD5844	Phase 1
0.7921	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7861	Intermediate Similarity	NPD7680	Approved
0.7853	Intermediate Similarity	NPD7808	Phase 3
0.7812	Intermediate Similarity	NPD7266	Discontinued
0.7803	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7802	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7797	Intermediate Similarity	NPD7251	Discontinued
0.7765	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.774	Intermediate Similarity	NPD6797	Phase 2
0.7727	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7697	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7697	Intermediate Similarity	NPD7685	Pre-registration
0.7669	Intermediate Similarity	NPD8166	Discontinued
0.7665	Intermediate Similarity	NPD1653	Approved
0.7657	Intermediate Similarity	NPD6166	Phase 2
0.7657	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7657	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7654	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.764	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7619	Intermediate Similarity	NPD7458	Discontinued
0.7614	Intermediate Similarity	NPD7473	Discontinued
0.7598	Intermediate Similarity	NPD6559	Discontinued
0.7571	Intermediate Similarity	NPD3818	Discontinued
0.7561	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7544	Intermediate Similarity	NPD1465	Phase 2
0.7543	Intermediate Similarity	NPD6232	Discontinued
0.7516	Intermediate Similarity	NPD7097	Phase 1
0.7487	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7487	Intermediate Similarity	NPD7783	Phase 2
0.7486	Intermediate Similarity	NPD6959	Discontinued
0.7474	Intermediate Similarity	NPD8151	Discontinued
0.7473	Intermediate Similarity	NPD7090	Clinical (unspecified phase)
0.7455	Intermediate Similarity	NPD4628	Phase 3
0.7455	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7455	Intermediate Similarity	NPD4110	Phase 3
0.7442	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7438	Intermediate Similarity	NPD3620	Phase 2
0.7438	Intermediate Similarity	NPD4060	Phase 1
0.7438	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.7425	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7423	Intermediate Similarity	NPD6099	Approved
0.7423	Intermediate Similarity	NPD6100	Approved
0.7414	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.7412	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7384	Intermediate Similarity	NPD1934	Approved
0.7345	Intermediate Similarity	NPD3787	Discontinued
0.7341	Intermediate Similarity	NPD7819	Suspended
0.7329	Intermediate Similarity	NPD1613	Approved
0.7329	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7312	Intermediate Similarity	NPD7985	Registered
0.7306	Intermediate Similarity	NPD7435	Discontinued
0.7289	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7284	Intermediate Similarity	NPD6355	Discontinued
0.7273	Intermediate Similarity	NPD5763	Approved
0.7273	Intermediate Similarity	NPD5762	Approved
0.7267	Intermediate Similarity	NPD8032	Phase 2
0.7246	Intermediate Similarity	NPD7003	Approved
0.7235	Intermediate Similarity	NPD6273	Approved
0.7222	Intermediate Similarity	NPD4140	Approved
0.7216	Intermediate Similarity	NPD7696	Phase 3
0.7216	Intermediate Similarity	NPD7698	Approved
0.7216	Intermediate Similarity	NPD7075	Discontinued
0.7216	Intermediate Similarity	NPD7697	Approved
0.7212	Intermediate Similarity	NPD2438	Suspended
0.7205	Intermediate Similarity	NPD6798	Discontinued
0.7205	Intermediate Similarity	NPD1699	Clinical (unspecified phase)
0.7205	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7204	Intermediate Similarity	NPD8150	Discontinued
0.72	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7182	Intermediate Similarity	NPD3751	Discontinued
0.7179	Intermediate Similarity	NPD8320	Phase 1
0.7179	Intermediate Similarity	NPD8319	Approved
0.7176	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.7172	Intermediate Similarity	NPD7874	Approved
0.7172	Intermediate Similarity	NPD7875	Clinical (unspecified phase)
0.7169	Intermediate Similarity	NPD6003	Clinical (unspecified phase)
0.7169	Intermediate Similarity	NPD6002	Phase 3
0.7169	Intermediate Similarity	NPD6004	Phase 3
0.7169	Intermediate Similarity	NPD6005	Phase 3
0.7169	Intermediate Similarity	NPD6006	Clinical (unspecified phase)
0.7168	Intermediate Similarity	NPD7028	Phase 2
0.7165	Intermediate Similarity	NPD6823	Phase 2
0.7157	Intermediate Similarity	NPD7701	Phase 2
0.715	Intermediate Similarity	NPD6778	Approved
0.715	Intermediate Similarity	NPD6782	Approved
0.715	Intermediate Similarity	NPD6777	Approved
0.715	Intermediate Similarity	NPD6779	Approved
0.715	Intermediate Similarity	NPD6781	Approved
0.715	Intermediate Similarity	NPD6776	Approved
0.715	Intermediate Similarity	NPD6780	Approved
0.7143	Intermediate Similarity	NPD3027	Phase 3
0.7143	Intermediate Similarity	NPD7095	Approved
0.7135	Intermediate Similarity	NPD5494	Approved
0.7135	Intermediate Similarity	NPD7699	Phase 2
0.7135	Intermediate Similarity	NPD7700	Phase 2
0.7125	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.711	Intermediate Similarity	NPD3226	Approved
0.7102	Intermediate Similarity	NPD3817	Phase 2
0.7101	Intermediate Similarity	NPD6190	Approved
0.7099	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7092	Intermediate Similarity	NPD7870	Phase 2
0.7092	Intermediate Similarity	NPD7871	Phase 2
0.709	Intermediate Similarity	NPD2488	Approved
0.709	Intermediate Similarity	NPD2490	Approved
0.7087	Intermediate Similarity	NPD5619	Clinical (unspecified phase)
0.7081	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7076	Intermediate Similarity	NPD2534	Approved
0.7076	Intermediate Similarity	NPD2533	Approved
0.7076	Intermediate Similarity	NPD2532	Approved
0.7074	Intermediate Similarity	NPD7906	Approved
0.7073	Intermediate Similarity	NPD5735	Approved
0.707	Intermediate Similarity	NPD3705	Approved
0.707	Intermediate Similarity	NPD1091	Approved
0.7069	Intermediate Similarity	NPD4380	Phase 2
0.7066	Intermediate Similarity	NPD2346	Discontinued
0.7062	Intermediate Similarity	NPD7768	Phase 2
0.7056	Intermediate Similarity	NPD7229	Phase 3
0.7055	Intermediate Similarity	NPD6233	Phase 2
0.7055	Intermediate Similarity	NPD6663	Approved
0.705	Intermediate Similarity	NPD7801	Approved
0.7045	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7045	Intermediate Similarity	NPD2801	Approved
0.7044	Intermediate Similarity	NPD1283	Approved
0.7044	Intermediate Similarity	NPD8651	Approved
0.7043	Intermediate Similarity	NPD7311	Approved
0.7043	Intermediate Similarity	NPD7312	Approved
0.7043	Intermediate Similarity	NPD7313	Approved
0.7043	Intermediate Similarity	NPD7310	Approved
0.7041	Intermediate Similarity	NPD7982	Clinical (unspecified phase)
0.7029	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7026	Intermediate Similarity	NPD2493	Approved
0.7026	Intermediate Similarity	NPD2494	Approved
0.7021	Intermediate Similarity	NPD8434	Phase 2
0.7019	Intermediate Similarity	NPD5736	Approved
0.7012	Intermediate Similarity	NPD2979	Phase 3
0.7005	Intermediate Similarity	NPD4583	Approved
0.7005	Intermediate Similarity	NPD4582	Approved
0.7005	Intermediate Similarity	NPD7309	Approved
0.6994	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6994	Remote Similarity	NPD6859	Clinical (unspecified phase)
0.6982	Remote Similarity	NPD7421	Clinical (unspecified phase)
0.6979	Remote Similarity	NPD6535	Approved
0.6979	Remote Similarity	NPD6534	Approved
0.6978	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6978	Remote Similarity	NPD2489	Approved
0.6978	Remote Similarity	NPD27	Approved
0.6977	Remote Similarity	NPD4160	Clinical (unspecified phase)
0.6975	Remote Similarity	NPD4908	Phase 1
0.697	Remote Similarity	NPD5123	Clinical (unspecified phase)
0.697	Remote Similarity	NPD5124	Phase 1
0.6961	Remote Similarity	NPD3051	Approved
0.6954	Remote Similarity	NPD4004	Approved
0.6954	Remote Similarity	NPD4002	Approved
0.6943	Remote Similarity	NPD1778	Approved
0.6941	Remote Similarity	NPD3750	Approved
0.6939	Remote Similarity	NPD3450	Approved
0.6939	Remote Similarity	NPD3452	Approved
0.6937	Remote Similarity	NPD6696	Suspended
0.6933	Remote Similarity	NPD4625	Phase 3
0.6932	Remote Similarity	NPD7411	Suspended
0.6931	Remote Similarity	NPD4663	Approved
0.6928	Remote Similarity	NPD6653	Approved
0.6923	Remote Similarity	NPD2969	Approved
0.6923	Remote Similarity	NPD2970	Approved
0.6914	Remote Similarity	NPD2861	Phase 2
0.6893	Remote Similarity	NPD6801	Discontinued
0.6885	Remote Similarity	NPD4481	Phase 3
0.6879	Remote Similarity	NPD7446	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD6599	Discontinued
0.6872	Remote Similarity	NPD3882	Suspended
0.6865	Remote Similarity	NPD8470	Clinical (unspecified phase)
0.6862	Remote Similarity	NPD4578	Approved
0.6862	Remote Similarity	NPD4577	Approved
0.6855	Remote Similarity	NPD1281	Approved
0.6852	Remote Similarity	NPD6917	Clinical (unspecified phase)
0.6851	Remote Similarity	NPD4666	Phase 3
0.6845	Remote Similarity	NPD7033	Discontinued
0.6839	Remote Similarity	NPD6213	Phase 3
0.6839	Remote Similarity	NPD6214	Clinical (unspecified phase)
0.6839	Remote Similarity	NPD6212	Phase 3
0.6836	Remote Similarity	NPD6677	Suspended

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