NPASS Compound

Structure

NPC206003 OpenBabel07101718312D 63 71 0 0 1 0 0 0 0 0999 V2000 2.4271 2.7634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0880 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8966 1.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2219 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3559 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7226 1.1810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8200 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2219 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9540 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3559 0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9135 0.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9540 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -1.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8822 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9540 -3.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4181 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7045 2.5823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6180 2.1756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0880 -2.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8200 -2.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3559 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2219 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4899 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.8822 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8200 -4.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.4181 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.7482 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8200 -5.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2841 -1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.7482 -2.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.6861 -5.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.8822 -2.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5521 -5.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2841 -2.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.4181 -2.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.0162 -2.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.5521 -4.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.5521 -2.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0880 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4899 0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.7482 0.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0880 -4.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2841 0.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -14.6143 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9540 -5.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1502 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -14.6143 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6861 -6.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.8822 -3.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4181 -5.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 1.9945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6861 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.0162 -1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6861 -3.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5521 -1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1502 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4181 -3.8090 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 2 20 1 0 0 0 0 5 6 1 0 0 0 0 5 21 1 0 0 0 0 7 12 1 0 0 0 0 7 19 1 0 0 0 0 8 10 1 0 0 0 0 8 22 1 0 0 0 0 9 11 1 0 0 0 0 9 24 1 0 0 0 0 10 43 1 0 0 0 0 11 44 1 0 0 0 0 13 21 1 0 0 0 0 13 22 1 0 0 0 0 14 25 1 0 0 0 0 15 46 1 0 0 0 0 16 47 1 0 0 0 0 17 48 1 0 0 0 0 18 19 1 0 0 0 0 18 56 1 0 0 0 0 19 1 1 1 0 0 0 20 30 1 0 0 0 0 20 45 1 6 0 0 0 21 43 1 6 0 0 0 22 57 1 1 0 0 0 23 6 1 6 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 24 43 1 1 0 0 0 25 44 1 1 0 0 0 26 14 1 1 0 0 0 26 30 1 0 0 0 0 26 63 1 0 0 0 0 27 15 1 1 0 0 0 27 31 1 0 0 0 0 27 58 1 0 0 0 0 28 16 1 6 0 0 0 28 32 1 0 0 0 0 28 59 1 0 0 0 0 29 17 1 1 0 0 0 29 33 1 0 0 0 0 29 60 1 0 0 0 0 30 44 1 1 0 0 0 31 34 1 0 0 0 0 31 49 1 6 0 0 0 32 35 1 0 0 0 0 32 50 1 1 0 0 0 33 38 1 0 0 0 0 33 51 1 1 0 0 0 34 36 1 0 0 0 0 34 52 1 1 0 0 0 35 37 1 0 0 0 0 35 53 1 6 0 0 0 36 40 1 0 0 0 0 36 54 1 6 0 0 0 37 41 1 0 0 0 0 37 55 1 1 0 0 0 38 39 1 0 0 0 0 38 61 1 1 0 0 0 39 42 1 0 0 0 0 39 62 1 6 0 0 0 40 58 1 0 0 0 0 40 61 1 1 0 0 0 41 59 1 0 0 0 0 41 62 1 6 0 0 0 42 57 1 1 0 0 0 42 60 1 0 0 0 0 43 3 1 1 0 0 0 44 4 1 1 0 0 0 45 12 1 1 0 0 0 45 56 1 0 0 0 0 45 63 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	902.49
Volume:	868.092
LogP:	1.408
LogD:	2.522
LogS:	-3.262
# Rotatable Bonds:	9
TPSA:	276.14
# H-Bond Aceptor:	18
# H-Bond Donor:	10
# Rings:	9
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.128
Synthetic Accessibility Score:	6.689
Fsp3:	1.0
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:	-6.331
MDCK Permeability:	0.00025077478494495153
Pgp-inhibitor:	0.426
Pgp-substrate:	0.959
Human Intestinal Absorption (HIA):	0.998
20% Bioavailability (F20%):	0.045
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.038
Plasma Protein Binding (PPB):	48.50399398803711%
Volume Distribution (VD):	0.077
Pgp-substrate:	10.264876365661621%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.212
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.069
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.004
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.045
CYP3A4-inhibitor:	0.011
CYP3A4-substrate:	0.017

ADMET: Excretion

Clearance (CL):	0.882
Half-life (T1/2):	0.841

ADMET: Toxicity

hERG Blockers:	0.859
Human Hepatotoxicity (H-HT):	0.137
Drug-inuced Liver Injury (DILI):	0.024
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.084
Maximum Recommended Daily Dose:	0.015
Skin Sensitization:	0.959
Carcinogencity:	0.255
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC206003

Natural Product ID:	NPC206003
*Common Name:**	DKEFDSJGKPNAQN-XDDGKFFLSA-N
IUPAC Name:	n.a.
Synonyms:	25(S)-Schidigera-Saponin D3
Standard InCHIKey:	DKEFDSJGKPNAQN-XDDGKFFLSA-N
Standard InCHI:	InChI=1S/C45H74O18/c1-19-7-12-45(56-18-19)20(2)30-26(63-45)14-25-23-6-5-21-13-22(8-10-43(21,3)24(23)9-11-44(25,30)4)57-42-39(62-41-37(55)35(53)32(50)28(16-47)59-41)38(33(51)29(17-48)60-42)61-40-36(54)34(52)31(49)27(15-46)58-40/h19-42,46-55H,5-18H2,1-4H3/t19-,20-,21+,22-,23+,24-,25-,26-,27+,28+,29+,30-,31+,32+,33-,34-,35-,36+,37+,38-,39+,40-,41-,42+,43-,44-,45+/m0/s1
SMILES:	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@@H](C2)CC[C@@H]2[C@@H]3CC[C@]3([C@H]2C[C@H]2[C@@H]3[C@H](C)[C@]3(O2)CC[C@@H](CO3)C)C)C)[C@@H]([C@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL452382
PubChem CID:	21603425
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal 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
NPO1943	Yucca schidigera	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757713]
NPO1943	Yucca schidigera	Species	Asparagaceae	Eukaryota	bark	n.a.	n.a.	PMID[15165156]
NPO1943	Yucca schidigera	Species	Asparagaceae	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
MIC	6

Activity Type	# Activity
Organism	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	25.0	ug.mL-1	PMID[570850]
NPT772	Organism	Pichia anomala	Wickerhamomyces anomalus	MIC	=	3.13	ug.mL-1	PMID[570850]
NPT5425	Organism	Pichia nakazawae	Pichia nakazawae	MIC	=	6.25	ug.mL-1	PMID[570850]
NPT5427	Organism	Hanseniaspora uvarum	Hanseniaspora uvarum	MIC	=	50.0	ug.mL-1	PMID[570850]
NPT5426	Organism	Debaryomyces hansenii	Debaryomyces hansenii	MIC	=	6.25	ug.mL-1	PMID[570850]
NPT312	Organism	Saccharomyces cerevisiae	Saccharomyces cerevisiae	MIC	=	12.5	ug.mL-1	PMID[570850]

☑ 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 NPC206003 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	567
0.1-0.2	5213
0.2-0.3	14518
0.3-0.4	10037
0.4-0.5	5583
0.5-0.6	3512
0.6-0.7	1877
0.7-0.8	913
0.8-0.85	173
0.85-0.9	159
0.9-0.95	43
0.95-1	102

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC473727
1.0	High Similarity	NPC6295
1.0	High Similarity	NPC473610
1.0	High Similarity	NPC107962
1.0	High Similarity	NPC19400
1.0	High Similarity	NPC107188
1.0	High Similarity	NPC475351
1.0	High Similarity	NPC211354
0.9888	High Similarity	NPC128572
0.9888	High Similarity	NPC184617
0.9888	High Similarity	NPC132080
0.9888	High Similarity	NPC195297
0.9888	High Similarity	NPC475643
0.9888	High Similarity	NPC84111
0.9888	High Similarity	NPC103616
0.9888	High Similarity	NPC30856
0.9888	High Similarity	NPC232037
0.9888	High Similarity	NPC473601
0.9888	High Similarity	NPC470866
0.9888	High Similarity	NPC475625
0.9888	High Similarity	NPC116756
0.9888	High Similarity	NPC287483
0.9888	High Similarity	NPC470864
0.9888	High Similarity	NPC97700
0.9888	High Similarity	NPC160426
0.9888	High Similarity	NPC284104
0.9888	High Similarity	NPC98018
0.9888	High Similarity	NPC470865
0.9888	High Similarity	NPC470863
0.9886	High Similarity	NPC291203
0.9886	High Similarity	NPC471464
0.9886	High Similarity	NPC264101
0.9886	High Similarity	NPC217205
0.9778	High Similarity	NPC476112
0.9778	High Similarity	NPC307534
0.9778	High Similarity	NPC470861
0.9778	High Similarity	NPC274200
0.9778	High Similarity	NPC232611
0.9778	High Similarity	NPC115165
0.9778	High Similarity	NPC303069
0.9778	High Similarity	NPC83137
0.9778	High Similarity	NPC470862
0.9778	High Similarity	NPC51520
0.9773	High Similarity	NPC477451
0.9773	High Similarity	NPC325828
0.9773	High Similarity	NPC177834
0.9773	High Similarity	NPC477547
0.9773	High Similarity	NPC141769
0.9773	High Similarity	NPC250393
0.9773	High Similarity	NPC249204
0.9773	High Similarity	NPC234352
0.9773	High Similarity	NPC48339
0.9773	High Similarity	NPC297348
0.967	High Similarity	NPC473518
0.967	High Similarity	NPC291548
0.9667	High Similarity	NPC139271
0.9667	High Similarity	NPC304011
0.9667	High Similarity	NPC121453
0.9663	High Similarity	NPC131693
0.9663	High Similarity	NPC294686
0.9663	High Similarity	NPC222731
0.9663	High Similarity	NPC473851
0.9663	High Similarity	NPC174024
0.9663	High Similarity	NPC291547
0.9663	High Similarity	NPC312678
0.9663	High Similarity	NPC253268
0.9663	High Similarity	NPC179859
0.9663	High Similarity	NPC475436
0.9556	High Similarity	NPC474399
0.9551	High Similarity	NPC137004
0.9551	High Similarity	NPC88962
0.9551	High Similarity	NPC144790
0.9551	High Similarity	NPC149400
0.9551	High Similarity	NPC172838
0.9444	High Similarity	NPC473774
0.9444	High Similarity	NPC252253
0.9444	High Similarity	NPC45959
0.9444	High Similarity	NPC305418
0.9444	High Similarity	NPC24960
0.9348	High Similarity	NPC477223
0.9348	High Similarity	NPC477222
0.9326	High Similarity	NPC473542
0.9326	High Similarity	NPC65550
0.9239	High Similarity	NPC476510
0.9239	High Similarity	NPC142264
0.9222	High Similarity	NPC5632
0.9222	High Similarity	NPC204881
0.9222	High Similarity	NPC473830
0.9222	High Similarity	NPC210759
0.9222	High Similarity	NPC307167
0.9222	High Similarity	NPC149966
0.9222	High Similarity	NPC229801
0.914	High Similarity	NPC475207
0.914	High Similarity	NPC233649
0.914	High Similarity	NPC470028
0.914	High Similarity	NPC470591
0.914	High Similarity	NPC210157
0.9121	High Similarity	NPC473726
0.9121	High Similarity	NPC167644
0.9121	High Similarity	NPC311246
0.9101	High Similarity	NPC281004
0.9053	High Similarity	NPC475574
0.9043	High Similarity	NPC473616
0.9022	High Similarity	NPC3538
0.9022	High Similarity	NPC309866
0.9022	High Similarity	NPC175
0.9022	High Similarity	NPC477224
0.9022	High Similarity	NPC113500
0.9	High Similarity	NPC20822
0.9	High Similarity	NPC82955
0.9	High Similarity	NPC102725
0.9	High Similarity	NPC131466
0.9	High Similarity	NPC473472
0.8925	High Similarity	NPC92196
0.8925	High Similarity	NPC473064
0.8925	High Similarity	NPC477494
0.8925	High Similarity	NPC473065
0.8925	High Similarity	NPC473067
0.8901	High Similarity	NPC279329
0.8901	High Similarity	NPC223143
0.8889	High Similarity	NPC92890
0.8889	High Similarity	NPC202898
0.8889	High Similarity	NPC475319
0.8889	High Similarity	NPC49032
0.8889	High Similarity	NPC125324
0.8889	High Similarity	NPC51172
0.8854	High Similarity	NPC476512
0.8854	High Similarity	NPC472081
0.8854	High Similarity	NPC108227
0.8842	High Similarity	NPC473638
0.883	High Similarity	NPC237071
0.883	High Similarity	NPC203434
0.883	High Similarity	NPC238796
0.883	High Similarity	NPC296936
0.8817	High Similarity	NPC77717
0.8817	High Similarity	NPC471373
0.8817	High Similarity	NPC253611
0.8817	High Similarity	NPC267238
0.8817	High Similarity	NPC148593
0.8804	High Similarity	NPC293609
0.8804	High Similarity	NPC36372
0.8804	High Similarity	NPC473637
0.8804	High Similarity	NPC476668
0.88	High Similarity	NPC220836
0.88	High Similarity	NPC151134
0.88	High Similarity	NPC233433
0.88	High Similarity	NPC473817
0.88	High Similarity	NPC94086
0.88	High Similarity	NPC92297
0.88	High Similarity	NPC273002
0.8778	High Similarity	NPC43912
0.8778	High Similarity	NPC140446
0.8763	High Similarity	NPC470029
0.8763	High Similarity	NPC310138
0.8763	High Similarity	NPC80191
0.8763	High Similarity	NPC114700
0.8763	High Similarity	NPC134967
0.8763	High Similarity	NPC310031
0.8723	High Similarity	NPC471425
0.8723	High Similarity	NPC189575
0.8723	High Similarity	NPC471429
0.8723	High Similarity	NPC205129
0.8723	High Similarity	NPC471424
0.8723	High Similarity	NPC106701
0.8713	High Similarity	NPC470867
0.871	High Similarity	NPC18724
0.871	High Similarity	NPC470623
0.871	High Similarity	NPC323231
0.871	High Similarity	NPC476669
0.871	High Similarity	NPC277774
0.871	High Similarity	NPC224003
0.871	High Similarity	NPC171741
0.8687	High Similarity	NPC215408
0.8673	High Similarity	NPC476837
0.8673	High Similarity	NPC97260
0.8673	High Similarity	NPC139181
0.866	High Similarity	NPC476839
0.866	High Similarity	NPC476838
0.866	High Similarity	NPC477225
0.8652	High Similarity	NPC227260
0.8617	High Similarity	NPC475325
0.8617	High Similarity	NPC30687
0.8617	High Similarity	NPC473503
0.8602	High Similarity	NPC59006
0.86	High Similarity	NPC54619
0.8557	High Similarity	NPC20028
0.8556	High Similarity	NPC290612
0.8556	High Similarity	NPC232044
0.8556	High Similarity	NPC273290
0.8526	High Similarity	NPC57964
0.8526	High Similarity	NPC94582
0.8526	High Similarity	NPC469710
0.8515	High Similarity	NPC128123
0.8454	Intermediate Similarity	NPC209798
0.8454	Intermediate Similarity	NPC471375
0.8454	Intermediate Similarity	NPC471374
0.8447	Intermediate Similarity	NPC92710
0.8447	Intermediate Similarity	NPC476547
0.8438	Intermediate Similarity	NPC473287
0.8431	Intermediate Similarity	NPC300557

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 NPC206003 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	546
0.1-0.2	4691
0.2-0.3	2784
0.3-0.4	586
0.4-0.5	337
0.5-0.6	156
0.6-0.7	32
0.7-0.8	15
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9773	High Similarity	NPD8171	Discontinued
0.8776	High Similarity	NPD8170	Clinical (unspecified phase)
0.8409	Intermediate Similarity	NPD6928	Phase 2
0.7615	Intermediate Similarity	NPD8133	Approved
0.7522	Intermediate Similarity	NPD8377	Approved
0.7522	Intermediate Similarity	NPD8294	Approved
0.7456	Intermediate Similarity	NPD8378	Approved
0.7456	Intermediate Similarity	NPD8296	Approved
0.7456	Intermediate Similarity	NPD8380	Approved
0.7456	Intermediate Similarity	NPD8335	Approved
0.7456	Intermediate Similarity	NPD8379	Approved
0.7426	Intermediate Similarity	NPD7991	Discontinued
0.7304	Intermediate Similarity	NPD8033	Approved
0.7043	Intermediate Similarity	NPD7328	Approved
0.7043	Intermediate Similarity	NPD7327	Approved
0.6983	Remote Similarity	NPD7516	Approved
0.6935	Remote Similarity	NPD8450	Suspended
0.6889	Remote Similarity	NPD4267	Clinical (unspecified phase)
0.6855	Remote Similarity	NPD8449	Approved
0.6774	Remote Similarity	NPD1810	Approved
0.6774	Remote Similarity	NPD1811	Approved
0.6757	Remote Similarity	NPD6412	Phase 2
0.6639	Remote Similarity	NPD7507	Approved
0.6637	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.6583	Remote Similarity	NPD7503	Approved
0.6581	Remote Similarity	NPD6940	Discontinued
0.6549	Remote Similarity	NPD8174	Phase 2
0.6525	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.648	Remote Similarity	NPD7319	Approved
0.6452	Remote Similarity	NPD4787	Phase 1
0.6452	Remote Similarity	NPD2687	Approved
0.6452	Remote Similarity	NPD2254	Approved
0.6452	Remote Similarity	NPD2686	Approved
0.64	Remote Similarity	NPD7736	Approved
0.6364	Remote Similarity	NPD6123	Approved
0.6341	Remote Similarity	NPD8328	Phase 3
0.6337	Remote Similarity	NPD3669	Approved
0.6337	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6327	Remote Similarity	NPD6697	Approved
0.6327	Remote Similarity	NPD6118	Approved
0.6327	Remote Similarity	NPD6115	Approved
0.6327	Remote Similarity	NPD6114	Approved
0.6277	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.626	Remote Similarity	NPD6370	Approved
0.6224	Remote Similarity	NPD6116	Phase 1
0.619	Remote Similarity	NPD8293	Discontinued
0.6122	Remote Similarity	NPD6117	Approved
0.6098	Remote Similarity	NPD6054	Approved
0.6098	Remote Similarity	NPD6059	Approved
0.6082	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6042	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.6042	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.5983	Remote Similarity	NPD6686	Approved
0.5978	Remote Similarity	NPD371	Approved
0.5952	Remote Similarity	NPD6067	Discontinued
0.5938	Remote Similarity	NPD4244	Approved
0.5938	Remote Similarity	NPD4245	Approved
0.592	Remote Similarity	NPD6016	Approved
0.592	Remote Similarity	NPD6015	Approved
0.5906	Remote Similarity	NPD7492	Approved
0.5882	Remote Similarity	NPD7525	Registered
0.5873	Remote Similarity	NPD5988	Approved
0.5872	Remote Similarity	NPD8034	Phase 2
0.5872	Remote Similarity	NPD8035	Phase 2
0.5862	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.5859	Remote Similarity	NPD3702	Approved
0.5859	Remote Similarity	NPD6616	Approved
0.5859	Remote Similarity	NPD3703	Phase 2
0.5857	Remote Similarity	NPD7625	Phase 1
0.5833	Remote Similarity	NPD3698	Phase 2
0.5833	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.5814	Remote Similarity	NPD7078	Approved
0.5794	Remote Similarity	NPD8516	Approved
0.5794	Remote Similarity	NPD8517	Approved
0.5794	Remote Similarity	NPD8515	Approved
0.5739	Remote Similarity	NPD1700	Approved
0.573	Remote Similarity	NPD2267	Suspended
0.5714	Remote Similarity	NPD5777	Approved
0.5702	Remote Similarity	NPD7638	Approved
0.5682	Remote Similarity	NPD7346	Approved
0.5673	Remote Similarity	NPD1779	Approved
0.5673	Remote Similarity	NPD1780	Approved
0.5669	Remote Similarity	NPD8513	Phase 3
0.5656	Remote Similarity	NPD6882	Approved
0.5656	Remote Similarity	NPD8297	Approved
0.5652	Remote Similarity	NPD7640	Approved
0.5652	Remote Similarity	NPD7639	Approved
0.5649	Remote Similarity	NPD6033	Approved
0.5648	Remote Similarity	NPD7524	Approved
0.5631	Remote Similarity	NPD7645	Phase 2
0.563	Remote Similarity	NPD7646	Clinical (unspecified phase)
0.5612	Remote Similarity	NPD4789	Approved
0.5607	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.56	Remote Similarity	NPD6009	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