NPASS Compound

Structure

CID235405 OpenBabel06191716032D 76 84 0 0 1 0 0 0 0 0999 V2000 3.0616 -4.3147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0734 -4.3147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0616 2.3382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0734 2.3382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7117 -0.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8558 1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8558 0.4941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8558 -1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8558 1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4233 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5675 -0.4941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4233 -2.9647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7117 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4233 -1.9765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5675 -0.4941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7117 -2.9647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4142 5.4353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7025 -1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6275 -3.8026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8558 -1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7117 -1.9765 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4142 4.4471 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8467 -0.9882 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2084 -3.0031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7117 0.9882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8558 -0.4941 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4233 0.9882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2700 3.9529 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8467 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.1966 -3.0031 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2700 2.9647 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9909 0.4941 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9909 -0.4941 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5020 -2.0632 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.4142 2.4706 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1350 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1350 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8467 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8467 0.9882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7025 1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7025 -1.4824 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.5584 2.9647 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1350 -0.9882 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1350 0.9882 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4233 -0.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5675 -3.4588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5675 1.4824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7117 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8558 -0.4941 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5675 -1.4824 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2700 5.9294 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5584 -0.9882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0295 -4.7054 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1259 4.4471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7025 0.4941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7775 -3.8026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1259 2.4706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9909 1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9909 -1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4419 -1.7578 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4142 1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2792 0.4941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2792 -0.4941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5584 0.9882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4233 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9030 -2.0632 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5584 3.9529 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9909 -1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2792 1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7025 -0.4941 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9909 1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7025 2.4706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2792 -1.4824 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 48 1 0 0 0 0 2 48 1 0 0 0 0 3 49 1 0 0 0 0 4 49 1 0 0 0 0 6 51 1 0 0 0 0 8 9 1 0 0 0 0 8 22 2 0 0 0 0 9 28 1 0 0 0 0 10 13 1 0 0 0 0 10 27 1 0 0 0 0 11 12 1 0 0 0 0 11 29 1 0 0 0 0 12 50 1 0 0 0 0 13 52 1 0 0 0 0 14 16 1 0 0 0 0 14 48 1 0 0 0 0 15 17 1 0 0 0 0 15 51 1 0 0 0 0 16 53 1 0 0 0 0 17 53 1 0 0 0 0 18 23 1 0 0 0 0 18 48 1 0 0 0 0 19 54 1 0 0 0 0 20 55 1 0 0 0 0 21 56 1 0 0 0 0 22 23 1 0 0 0 0 22 51 1 0 0 0 0 23 53 1 1 0 0 0 24 19 1 1 0 0 0 24 30 1 0 0 0 0 24 70 1 0 0 0 0 25 20 1 1 0 0 0 25 31 1 0 0 0 0 25 71 1 0 0 0 0 26 21 1 1 0 0 0 26 32 1 0 0 0 0 26 69 1 0 0 0 0 27 49 1 0 0 0 0 27 50 1 6 0 0 0 28 50 1 6 0 0 0 28 52 1 0 0 0 0 29 49 1 0 0 0 0 29 72 1 6 0 0 0 30 33 1 0 0 0 0 30 57 1 6 0 0 0 31 34 1 0 0 0 0 31 58 1 6 0 0 0 32 36 1 0 0 0 0 32 59 1 6 0 0 0 33 37 1 0 0 0 0 33 60 1 1 0 0 0 34 38 1 0 0 0 0 34 61 1 1 0 0 0 35 39 1 0 0 0 0 35 40 1 0 0 0 0 35 62 1 1 0 0 0 36 43 1 0 0 0 0 36 63 1 1 0 0 0 37 44 1 0 0 0 0 37 64 1 6 0 0 0 38 45 1 0 0 0 0 38 65 1 6 0 0 0 39 46 1 0 0 0 0 39 66 1 6 0 0 0 40 41 1 0 0 0 0 40 73 1 6 0 0 0 41 42 1 1 0 0 0 41 74 1 0 0 0 0 42 67 2 0 0 0 0 42 75 1 0 0 0 0 43 69 1 0 0 0 0 43 73 1 6 0 0 0 44 70 1 0 0 0 0 44 75 1 1 0 0 0 45 71 1 0 0 0 0 45 76 1 1 0 0 0 46 72 1 1 0 0 0 46 74 1 0 0 0 0 47 68 2 0 0 0 0 47 76 1 0 0 0 0 50 5 1 6 0 0 0 51 52 1 6 0 0 0 52 7 1 6 0 0 0 53 47 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1088.54
Volume:	1042.501
LogP:	2.003
LogD:	1.516
LogS:	-3.385
# Rotatable Bonds:	13
TPSA:	370.97
# H-Bond Aceptor:	23
# H-Bond Donor:	13
# Rings:	9
# Heavy Atoms:	23

MedChem Properties

QED Drug-Likeness Score:	0.061
Synthetic Accessibility Score:	6.745
Fsp3:	0.925
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.235
MDCK Permeability:	0.00032024469692260027
Pgp-inhibitor:	0.434
Pgp-substrate:	0.91
Human Intestinal Absorption (HIA):	0.979
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.066
Plasma Protein Binding (PPB):	69.54828643798828%
Volume Distribution (VD):	0.168
Pgp-substrate:	17.538244247436523%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.076
CYP2C19-inhibitor:	0.0
CYP2C19-substrate:	0.117
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.045
CYP3A4-inhibitor:	0.047
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	0.244
Half-life (T1/2):	0.586

ADMET: Toxicity

hERG Blockers:	0.048
Human Hepatotoxicity (H-HT):	0.164
Drug-inuced Liver Injury (DILI):	0.026
AMES Toxicity:	0.104
Rat Oral Acute Toxicity:	0.068
Maximum Recommended Daily Dose:	0.051
Skin Sensitization:	0.027
Carcinogencity:	0.014
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.079

Download Data

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

Natural Product: NPC235405

Natural Product ID:	NPC235405
*Common Name:**	Chikusetsusaponin-Ib
IUPAC Name:	[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (2S,3S,4R,5R,6R)-6-[[(3S,4aR,6aR,6bS,8aS,12aS,14aR,14bR)-4,4,6a,6b,11,11,14b-heptamethyl-8a-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxycarbonyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-3-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-4,5-dihydroxyoxane-2-carboxylate
Synonyms:	Chikusetsusaponin-Ib
Standard InCHIKey:	ZGUGZUGPYPBJAQ-CGGDTZFRSA-N
Standard InCHI:	InChI=1S/C53H84O23/c1-48(2)14-16-53(47(68)76-45-38(65)34(61)31(58)25(20-55)71-45)17-15-51(6)22(23(53)18-48)8-9-28-50(5)12-11-29(49(3,4)27(50)10-13-52(28,51)7)72-46-39(66)35(62)40(73-43-36(63)32(59)26(21-56)69-43)41(74-46)42(67)75-44-37(64)33(60)30(57)24(19-54)70-44/h8,23-41,43-46,54-66H,9-21H2,1-7H3/t23-,24+,25+,26-,27-,28+,29-,30+,31+,32-,33-,34-,35+,36+,37+,38+,39+,40-,41-,43-,44-,45-,46+,50-,51+,52+,53-/m0/s1
SMILES:	OC[C@@H]1O[C@H]([C@@H]([C@H]1O)O)O[C@@H]1[C@H](O[C@H]([C@@H]([C@H]1O)O)O[C@H]1CC[C@]2([C@H](C1(C)C)CC[C@@]1([C@@H]2CC=C2[C@@]1(C)CC[C@@]1([C@H]2CC(C)(C)CC1)C(=O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)C)C)C(=O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1773986
PubChem CID:	54587154
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350149]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[21417387]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[21417387]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28006911]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28202328]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005.2	Panax japonicus var. major (burk.) wu et feng	Varieties	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28005	Panax japonicus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28005	Panax japonicus	Species	Araliaceae	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	2

Activity Type	# Activity
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	1560.0	nM	PMID[484295]
NPT2	Others	Unspecified		IC50	=	1870.0	nM	PMID[484295]

☑ 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 NPC235405 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	281
0.1-0.2	1830
0.2-0.3	5527
0.3-0.4	10884
0.4-0.5	10165
0.5-0.6	6714
0.6-0.7	4119
0.7-0.8	1957
0.8-0.85	498
0.85-0.9	474
0.9-0.95	172
0.95-1	76

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC30735
1.0	High Similarity	NPC281148
0.9912	High Similarity	NPC235438
0.9912	High Similarity	NPC249848
0.9912	High Similarity	NPC470477
0.9912	High Similarity	NPC107966
0.9912	High Similarity	NPC40775
0.9826	High Similarity	NPC470218
0.9823	High Similarity	NPC223301
0.9823	High Similarity	NPC64715
0.9823	High Similarity	NPC297263
0.9823	High Similarity	NPC22956
0.9823	High Similarity	NPC171544
0.9823	High Similarity	NPC104372
0.9823	High Similarity	NPC301449
0.9823	High Similarity	NPC222580
0.9823	High Similarity	NPC114484
0.9823	High Similarity	NPC11242
0.9823	High Similarity	NPC62725
0.9823	High Similarity	NPC86222
0.9823	High Similarity	NPC159309
0.9823	High Similarity	NPC31838
0.9737	High Similarity	NPC187290
0.9737	High Similarity	NPC162574
0.9737	High Similarity	NPC475591
0.9737	High Similarity	NPC21691
0.9737	High Similarity	NPC213952
0.9737	High Similarity	NPC10607
0.9737	High Similarity	NPC4749
0.9737	High Similarity	NPC80986
0.9737	High Similarity	NPC236870
0.9735	High Similarity	NPC118440
0.9735	High Similarity	NPC236657
0.9655	High Similarity	NPC285091
0.9652	High Similarity	NPC283417
0.9652	High Similarity	NPC257211
0.9652	High Similarity	NPC200049
0.9652	High Similarity	NPC44716
0.9652	High Similarity	NPC478066
0.9652	High Similarity	NPC258617
0.9652	High Similarity	NPC2370
0.9652	High Similarity	NPC302543
0.9649	High Similarity	NPC302887
0.9649	High Similarity	NPC187618
0.9646	High Similarity	NPC180550
0.9646	High Similarity	NPC473884
0.9646	High Similarity	NPC475171
0.9646	High Similarity	NPC472949
0.9646	High Similarity	NPC39211
0.9646	High Similarity	NPC469945
0.9646	High Similarity	NPC192791
0.9646	High Similarity	NPC35405
0.9646	High Similarity	NPC208381
0.9646	High Similarity	NPC6377
0.9646	High Similarity	NPC11551
0.9646	High Similarity	NPC309780
0.9646	High Similarity	NPC114441
0.9646	High Similarity	NPC214484
0.9646	High Similarity	NPC157868
0.9569	High Similarity	NPC471963
0.9569	High Similarity	NPC247315
0.9569	High Similarity	NPC160452
0.9569	High Similarity	NPC33068
0.9569	High Similarity	NPC471962
0.9565	High Similarity	NPC313110
0.9565	High Similarity	NPC131469
0.9558	High Similarity	NPC105800
0.9558	High Similarity	NPC286347
0.9558	High Similarity	NPC232237
0.9487	High Similarity	NPC181066
0.9487	High Similarity	NPC475368
0.9487	High Similarity	NPC284449
0.9487	High Similarity	NPC469947
0.9483	High Similarity	NPC471961
0.9483	High Similarity	NPC262199
0.9483	High Similarity	NPC14617
0.9483	High Similarity	NPC471964
0.9483	High Similarity	NPC202666
0.9478	High Similarity	NPC31193
0.9478	High Similarity	NPC75417
0.9478	High Similarity	NPC242840
0.9474	High Similarity	NPC207738
0.9469	High Similarity	NPC224121
0.9402	High Similarity	NPC23275
0.9397	High Similarity	NPC471965
0.9391	High Similarity	NPC294112
0.9391	High Similarity	NPC473645
0.9386	High Similarity	NPC109588
0.9381	High Similarity	NPC37134
0.9381	High Similarity	NPC291903
0.9328	High Similarity	NPC470475
0.9298	High Similarity	NPC475119
0.9298	High Similarity	NPC473824
0.9298	High Similarity	NPC300419
0.9292	High Similarity	NPC475486
0.9292	High Similarity	NPC164389
0.9237	High Similarity	NPC130229
0.9231	High Similarity	NPC275343
0.9224	High Similarity	NPC144644
0.9224	High Similarity	NPC37860
0.9224	High Similarity	NPC110385
0.9224	High Similarity	NPC267694
0.9224	High Similarity	NPC142151
0.9224	High Similarity	NPC153673
0.9211	High Similarity	NPC75287
0.9211	High Similarity	NPC305267
0.9211	High Similarity	NPC26626
0.9211	High Similarity	NPC288205
0.9211	High Similarity	NPC476992
0.9211	High Similarity	NPC51465
0.9174	High Similarity	NPC134914
0.9174	High Similarity	NPC301639
0.9174	High Similarity	NPC45346
0.9174	High Similarity	NPC25998
0.9174	High Similarity	NPC264566
0.9174	High Similarity	NPC173435
0.9174	High Similarity	NPC478155
0.9174	High Similarity	NPC329993
0.9174	High Similarity	NPC478065
0.9174	High Similarity	NPC478064
0.9174	High Similarity	NPC475377
0.9174	High Similarity	NPC262796
0.9174	High Similarity	NPC172374
0.9174	High Similarity	NPC475167
0.9174	High Similarity	NPC476074
0.9167	High Similarity	NPC470476
0.9145	High Similarity	NPC275225
0.9145	High Similarity	NPC51099
0.9145	High Similarity	NPC293031
0.9145	High Similarity	NPC470478
0.9145	High Similarity	NPC68767
0.9138	High Similarity	NPC51564
0.9138	High Similarity	NPC25663
0.9138	High Similarity	NPC135849
0.913	High Similarity	NPC33012
0.913	High Similarity	NPC220160
0.913	High Similarity	NPC69811
0.913	High Similarity	NPC475514
0.913	High Similarity	NPC102505
0.913	High Similarity	NPC323359
0.913	High Similarity	NPC104137
0.913	High Similarity	NPC191827
0.913	High Similarity	NPC85154
0.913	High Similarity	NPC470876
0.913	High Similarity	NPC473452
0.913	High Similarity	NPC8524
0.913	High Similarity	NPC309223
0.913	High Similarity	NPC123522
0.913	High Similarity	NPC475209
0.913	High Similarity	NPC286457
0.9115	High Similarity	NPC257468
0.9115	High Similarity	NPC139044
0.9115	High Similarity	NPC104071
0.9115	High Similarity	NPC276093
0.9115	High Similarity	NPC102439
0.9115	High Similarity	NPC109079
0.9115	High Similarity	NPC1046
0.9115	High Similarity	NPC104400
0.9115	High Similarity	NPC475516
0.9115	High Similarity	NPC471383
0.9115	High Similarity	NPC292677
0.9115	High Similarity	NPC79718
0.9115	High Similarity	NPC80843
0.9115	High Similarity	NPC475504
0.9115	High Similarity	NPC469946
0.9115	High Similarity	NPC101744
0.9115	High Similarity	NPC473373
0.9115	High Similarity	NPC10320
0.9115	High Similarity	NPC324875
0.9098	High Similarity	NPC478154
0.9098	High Similarity	NPC476776
0.9098	High Similarity	NPC478153
0.9098	High Similarity	NPC478150
0.9098	High Similarity	NPC478152
0.9091	High Similarity	NPC141600
0.9091	High Similarity	NPC88311
0.9091	High Similarity	NPC11577
0.9091	High Similarity	NPC269484
0.9091	High Similarity	NPC252289
0.9091	High Similarity	NPC9470
0.9091	High Similarity	NPC115656
0.9091	High Similarity	NPC472267
0.9091	High Similarity	NPC305793
0.9091	High Similarity	NPC97918
0.9091	High Similarity	NPC280029
0.9091	High Similarity	NPC470518
0.9091	High Similarity	NPC1314
0.9091	High Similarity	NPC47995
0.9091	High Similarity	NPC265841
0.9091	High Similarity	NPC82380
0.9091	High Similarity	NPC252657
0.9091	High Similarity	NPC470912
0.9091	High Similarity	NPC107536
0.9091	High Similarity	NPC273878
0.9091	High Similarity	NPC244296
0.9091	High Similarity	NPC477196
0.906	High Similarity	NPC476991
0.9052	High Similarity	NPC473459
0.9052	High Similarity	NPC237191
0.9052	High Similarity	NPC475899

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 NPC235405 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	244
0.1-0.2	2083
0.2-0.3	4048
0.3-0.4	1762
0.4-0.5	546
0.5-0.6	255
0.6-0.7	152
0.7-0.8	55
0.8-0.85	3
0.85-0.9	0
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9483	High Similarity	NPD8328	Phase 3
0.9298	High Similarity	NPD8295	Clinical (unspecified phase)
0.8254	Intermediate Similarity	NPD7736	Approved
0.8205	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.8083	Intermediate Similarity	NPD8133	Approved
0.8065	Intermediate Similarity	NPD8515	Approved
0.8065	Intermediate Similarity	NPD8513	Phase 3
0.8065	Intermediate Similarity	NPD8517	Approved
0.8065	Intermediate Similarity	NPD8516	Approved
0.8031	Intermediate Similarity	NPD8293	Discontinued
0.7857	Intermediate Similarity	NPD6370	Approved
0.7769	Intermediate Similarity	NPD7319	Approved
0.7734	Intermediate Similarity	NPD7492	Approved
0.7698	Intermediate Similarity	NPD6054	Approved
0.7698	Intermediate Similarity	NPD6059	Approved
0.7674	Intermediate Similarity	NPD7507	Approved
0.7674	Intermediate Similarity	NPD6616	Approved
0.7615	Intermediate Similarity	NPD7078	Approved
0.7583	Intermediate Similarity	NPD6412	Phase 2
0.7559	Intermediate Similarity	NPD8294	Approved
0.7559	Intermediate Similarity	NPD6319	Approved
0.7559	Intermediate Similarity	NPD8377	Approved
0.7521	Intermediate Similarity	NPD6686	Approved
0.75	Intermediate Similarity	NPD8335	Approved
0.75	Intermediate Similarity	NPD8380	Approved
0.75	Intermediate Similarity	NPD8379	Approved
0.75	Intermediate Similarity	NPD8296	Approved
0.75	Intermediate Similarity	NPD6016	Approved
0.75	Intermediate Similarity	NPD8378	Approved
0.75	Intermediate Similarity	NPD6015	Approved
0.7442	Intermediate Similarity	NPD5988	Approved
0.7419	Intermediate Similarity	NPD8297	Approved
0.7419	Intermediate Similarity	NPD6882	Approved
0.7417	Intermediate Similarity	NPD8170	Clinical (unspecified phase)
0.7377	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.7364	Intermediate Similarity	NPD8033	Approved
0.735	Intermediate Similarity	NPD7902	Approved
0.7339	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7323	Intermediate Similarity	NPD6009	Approved
0.7317	Intermediate Similarity	NPD6373	Approved
0.7317	Intermediate Similarity	NPD6372	Approved
0.7241	Intermediate Similarity	NPD7748	Approved
0.7213	Intermediate Similarity	NPD6675	Approved
0.7213	Intermediate Similarity	NPD6402	Approved
0.7213	Intermediate Similarity	NPD7128	Approved
0.7213	Intermediate Similarity	NPD5739	Approved
0.72	Intermediate Similarity	NPD6649	Approved
0.72	Intermediate Similarity	NPD6650	Approved
0.7164	Intermediate Similarity	NPD6033	Approved
0.7132	Intermediate Similarity	NPD7327	Approved
0.7132	Intermediate Similarity	NPD7328	Approved
0.7097	Intermediate Similarity	NPD7320	Approved
0.7097	Intermediate Similarity	NPD6899	Approved
0.7097	Intermediate Similarity	NPD6881	Approved
0.7094	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7094	Intermediate Similarity	NPD7900	Approved
0.709	Intermediate Similarity	NPD8074	Phase 3
0.7087	Intermediate Similarity	NPD4632	Approved
0.7077	Intermediate Similarity	NPD7516	Approved
0.7069	Intermediate Similarity	NPD7515	Phase 2
0.7063	Intermediate Similarity	NPD8130	Phase 1
0.7016	Intermediate Similarity	NPD5701	Approved
0.7016	Intermediate Similarity	NPD5697	Approved
0.6984	Remote Similarity	NPD7290	Approved
0.6984	Remote Similarity	NPD6883	Approved
0.6984	Remote Similarity	NPD7102	Approved
0.697	Remote Similarity	NPD7503	Approved
0.6929	Remote Similarity	NPD6617	Approved
0.6929	Remote Similarity	NPD6847	Approved
0.6929	Remote Similarity	NPD6869	Approved
0.6923	Remote Similarity	NPD8035	Phase 2
0.6923	Remote Similarity	NPD8034	Phase 2
0.6905	Remote Similarity	NPD6012	Approved
0.6905	Remote Similarity	NPD6014	Approved
0.6905	Remote Similarity	NPD6013	Approved
0.6866	Remote Similarity	NPD7604	Phase 2
0.685	Remote Similarity	NPD4634	Approved
0.6842	Remote Similarity	NPD6921	Approved
0.6842	Remote Similarity	NPD5983	Phase 2
0.6825	Remote Similarity	NPD6011	Approved
0.6797	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6794	Remote Similarity	NPD7115	Discovery
0.678	Remote Similarity	NPD6411	Approved
0.6765	Remote Similarity	NPD6336	Discontinued
0.6741	Remote Similarity	NPD6067	Discontinued
0.6723	Remote Similarity	NPD6399	Phase 3
0.6723	Remote Similarity	NPD8171	Discontinued
0.6721	Remote Similarity	NPD7638	Approved
0.6721	Remote Similarity	NPD4225	Approved
0.6667	Remote Similarity	NPD6008	Approved
0.6667	Remote Similarity	NPD7639	Approved
0.6667	Remote Similarity	NPD7640	Approved
0.6641	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6639	Remote Similarity	NPD6083	Phase 2
0.6639	Remote Similarity	NPD4755	Approved
0.6639	Remote Similarity	NPD6084	Phase 2
0.661	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.661	Remote Similarity	NPD6101	Approved
0.6593	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.6591	Remote Similarity	NPD6274	Approved
0.6589	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6567	Remote Similarity	NPD7101	Approved
0.6567	Remote Similarity	NPD7100	Approved
0.6557	Remote Similarity	NPD4697	Phase 3
0.6552	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6544	Remote Similarity	NPD8080	Discontinued
0.6532	Remote Similarity	NPD4696	Approved
0.6532	Remote Similarity	NPD5286	Approved
0.6532	Remote Similarity	NPD5285	Approved
0.6532	Remote Similarity	NPD4700	Approved
0.65	Remote Similarity	NPD7983	Approved
0.6493	Remote Similarity	NPD6335	Approved
0.6471	Remote Similarity	NPD6909	Approved
0.6471	Remote Similarity	NPD6908	Approved
0.6471	Remote Similarity	NPD5328	Approved
0.6466	Remote Similarity	NPD6868	Approved
0.646	Remote Similarity	NPD7645	Phase 2
0.6454	Remote Similarity	NPD5956	Approved
0.6452	Remote Similarity	NPD5696	Approved
0.6446	Remote Similarity	NPD5778	Approved
0.6446	Remote Similarity	NPD5779	Approved
0.6434	Remote Similarity	NPD8450	Suspended
0.6429	Remote Similarity	NPD5224	Approved
0.6429	Remote Similarity	NPD4633	Approved
0.6429	Remote Similarity	NPD5226	Approved
0.6429	Remote Similarity	NPD5211	Phase 2
0.6429	Remote Similarity	NPD5225	Approved
0.6423	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.6423	Remote Similarity	NPD5222	Approved
0.6423	Remote Similarity	NPD5221	Approved
0.6418	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6418	Remote Similarity	NPD6317	Approved
0.6414	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.6406	Remote Similarity	NPD4768	Approved
0.6406	Remote Similarity	NPD4767	Approved
0.6387	Remote Similarity	NPD5737	Approved
0.6387	Remote Similarity	NPD6672	Approved
0.6378	Remote Similarity	NPD5174	Approved
0.6378	Remote Similarity	NPD5175	Approved
0.6371	Remote Similarity	NPD5173	Approved
0.637	Remote Similarity	NPD6314	Approved
0.637	Remote Similarity	NPD6313	Approved
0.6364	Remote Similarity	NPD8449	Approved
0.6364	Remote Similarity	NPD7799	Discontinued
0.6364	Remote Similarity	NPD6079	Approved
0.6357	Remote Similarity	NPD8448	Approved
0.6357	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6357	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6356	Remote Similarity	NPD3618	Phase 1
0.635	Remote Similarity	NPD6291	Clinical (unspecified phase)
0.6349	Remote Similarity	NPD5223	Approved
0.6345	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.6341	Remote Similarity	NPD5695	Phase 3
0.6338	Remote Similarity	NPD8392	Approved
0.6338	Remote Similarity	NPD8391	Approved
0.6338	Remote Similarity	NPD8390	Approved
0.6331	Remote Similarity	NPD8299	Approved
0.6331	Remote Similarity	NPD8342	Approved
0.6331	Remote Similarity	NPD8341	Approved
0.6331	Remote Similarity	NPD8340	Approved
0.6328	Remote Similarity	NPD5141	Approved
0.6316	Remote Similarity	NPD7329	Approved
0.6312	Remote Similarity	NPD8337	Approved
0.6312	Remote Similarity	NPD8336	Approved
0.6308	Remote Similarity	NPD4730	Approved
0.6308	Remote Similarity	NPD4729	Approved
0.6303	Remote Similarity	NPD3573	Approved
0.6286	Remote Similarity	NPD8451	Approved
0.6276	Remote Similarity	NPD8415	Approved
0.626	Remote Similarity	NPD5282	Discontinued
0.625	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.625	Remote Similarity	NPD4754	Approved
0.6212	Remote Similarity	NPD5248	Approved
0.6212	Remote Similarity	NPD5250	Approved
0.6212	Remote Similarity	NPD5247	Approved
0.6212	Remote Similarity	NPD5249	Phase 3
0.6212	Remote Similarity	NPD5251	Approved
0.6198	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6186	Remote Similarity	NPD4786	Approved
0.6183	Remote Similarity	NPD5128	Approved
0.6181	Remote Similarity	NPD7260	Phase 2
0.6172	Remote Similarity	NPD7632	Discontinued
0.616	Remote Similarity	NPD7839	Suspended
0.6154	Remote Similarity	NPD3667	Approved
0.6149	Remote Similarity	NPD6334	Approved
0.6149	Remote Similarity	NPD6333	Approved
0.6148	Remote Similarity	NPD46	Approved
0.6148	Remote Similarity	NPD6698	Approved
0.6143	Remote Similarity	NPD7829	Approved
0.6143	Remote Similarity	NPD7830	Approved
0.6138	Remote Similarity	NPD8338	Approved
0.6115	Remote Similarity	NPD8444	Approved
0.6103	Remote Similarity	NPD6940	Discontinued
0.6102	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6102	Remote Similarity	NPD3669	Approved
0.6094	Remote Similarity	NPD1700	Approved
0.6083	Remote Similarity	NPD7334	Approved
0.6083	Remote Similarity	NPD6409	Approved
0.6083	Remote Similarity	NPD5330	Approved
0.6083	Remote Similarity	NPD6098	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