NPASS Compound

Structure

CID299990 OpenBabel06191716102D 45 52 0 0 1 0 0 0 0 0999 V2000 -2.7905 2.1071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6498 -3.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6207 0.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3642 1.9868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8653 -1.4886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5132 -2.1887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4341 0.9840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5770 -0.9952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0054 -1.8474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8686 0.6878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0759 1.9606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9483 -3.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5261 2.0348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0823 -3.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3387 -2.3187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4213 1.1427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3124 0.3666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3338 1.4799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8143 -1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6998 0.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1507 0.9894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9368 -2.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9316 0.8290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8532 1.5624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9483 -2.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3601 -1.3648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2415 1.2078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8369 1.2736 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.7838 -2.0933 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.9079 0.1633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0745 1.0224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5225 -0.1943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2705 0.5344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8143 -0.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0823 -1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9483 -0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0823 -0.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8647 1.7290 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7838 -3.0933 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8388 -0.2020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9233 1.0893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5575 0.0758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1562 0.8848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5390 -0.7931 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 1 38 1 0 0 0 0 2 39 1 0 0 0 0 3 40 1 0 0 0 0 4 41 1 0 0 0 0 5 8 1 0 0 0 0 5 22 2 0 0 0 0 6 9 2 0 0 0 0 6 22 1 0 0 0 0 7 10 2 0 0 0 0 7 23 1 0 0 0 0 8 26 2 0 0 0 0 9 26 1 0 0 0 0 10 30 1 0 0 0 0 11 13 1 0 0 0 0 11 24 1 0 0 0 0 12 14 1 0 0 0 0 12 25 1 0 0 0 0 13 38 1 0 0 0 0 14 39 1 0 0 0 0 15 22 1 0 0 0 0 15 29 1 0 0 0 0 16 23 1 0 0 0 0 16 28 1 0 0 0 0 17 23 2 0 0 0 0 17 32 1 0 0 0 0 18 24 2 0 0 0 0 18 31 1 0 0 0 0 19 25 2 0 0 0 0 19 34 1 0 0 0 0 20 27 2 0 0 0 0 20 33 1 0 0 0 0 21 42 1 0 0 0 0 21 43 1 0 0 0 0 24 27 1 0 0 0 0 25 35 1 0 0 0 0 26 44 1 0 0 0 0 27 28 1 0 0 0 0 28 38 1 0 0 0 0 29 35 1 0 0 0 0 29 39 1 0 0 0 0 30 32 2 0 0 0 0 30 40 1 0 0 0 0 31 33 2 0 0 0 0 31 41 1 0 0 0 0 32 44 1 0 0 0 0 33 45 1 0 0 0 0 34 36 2 0 0 0 0 34 42 1 0 0 0 0 35 37 2 0 0 0 0 36 37 1 0 0 0 0 36 43 1 0 0 0 0 37 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	606.27
Volume:	623.154
LogP:	6.23
LogD:	3.895
LogS:	-5.85
# Rotatable Bonds:	2
TPSA:	61.86
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	9
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.245
Synthetic Accessibility Score:	5.81
Fsp3:	0.351
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.667
MDCK Permeability:	2.9049813747406006e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.317
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.857

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.384
Plasma Protein Binding (PPB):	93.28301239013672%
Volume Distribution (VD):	0.959
Pgp-substrate:	3.1959328651428223%

ADMET: Metabolism

CYP1A2-inhibitor:	0.083
CYP1A2-substrate:	0.955
CYP2C19-inhibitor:	0.197
CYP2C19-substrate:	0.976
CYP2C9-inhibitor:	0.039
CYP2C9-substrate:	0.605
CYP2D6-inhibitor:	0.268
CYP2D6-substrate:	0.965
CYP3A4-inhibitor:	0.399
CYP3A4-substrate:	0.955

ADMET: Excretion

Clearance (CL):	12.132
Half-life (T1/2):	0.097

ADMET: Toxicity

hERG Blockers:	0.981
Human Hepatotoxicity (H-HT):	0.032
Drug-inuced Liver Injury (DILI):	0.421
AMES Toxicity:	0.131
Rat Oral Acute Toxicity:	0.173
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.47
Carcinogencity:	0.346
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.497

Download Data

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

Natural Product: NPC299990

Natural Product ID:	NPC299990
*Common Name:**	YVPXVXANRNDGTA-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YVPXVXANRNDGTA-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C37H38N2O6/c1-38-13-11-24-18-31(41-4)33-20-27(24)28(38)16-23-7-10-30(40-3)32(17-23)44-26-8-5-22(6-9-26)15-29-35-25(12-14-39(29)2)19-34-36(37(35)45-33)43-21-42-34/h5-10,17-20,28-29H,11-16,21H2,1-4H3
SMILES:	CN1CCc2cc(c3cc2C1Cc1ccc(c(c1)Oc1ccc(cc1)CC1c2c(CCN1C)cc1c(c2O3)OCO1)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1473842
PubChem CID:	360849
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds

*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
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	stem	n.a.	PMID[21214233]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21214233]
NPO31374	Stephania cepharantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129063]
NPO19964	Stephania sasakii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31374	Stephania cepharantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9266	Stephania delavayi	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9266	Stephania delavayi	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19964	Stephania sasakii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO31374	Stephania cepharantha	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9266	Stephania delavayi	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9266	Stephania delavayi	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19964	Stephania sasakii	Species	Menispermaceae	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
Potency	13

Activity Type	# Activity
Individual Protein	9
Organism	2
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	=	1122.0	nM	PMID[519125]
NPT45	Individual Protein	Ubiquitin carboxyl-terminal hydrolase 2	Homo sapiens	Potency	=	10000.0	nM	PMID[519125]
NPT282	Individual Protein	MAP kinase ERK2	Homo sapiens	Potency	=	19952.6	nM	PMID[519125]
NPT109	Individual Protein	Cytochrome P450 3A4	Homo sapiens	Potency	=	39810.7	nM	PMID[519125]
NPT61	Individual Protein	Beta-glucocerebrosidase	Homo sapiens	Potency	n.a.	25118.9	nM	PMID[519125]
NPT1139	Individual Protein	Arachidonate 15-lipoxygenase, type II	Homo sapiens	Potency	n.a.	19952.6	nM	PMID[519125]
NPT444	Individual Protein	Ubiquitin carboxyl-terminal hydrolase 1	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[519125]
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	26608.6	nM	PMID[519125]
NPT2	Others	Unspecified		Potency	=	31622.8	nM	PMID[519125]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	5358.2	nM	PMID[519125]
NPT2	Others	Unspecified		Potency	n.a.	16136.6	nM	PMID[519125]

☑ 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 NPC299990 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	452
0.1-0.2	1959
0.2-0.3	9523
0.3-0.4	8891
0.4-0.5	6576
0.5-0.6	9990
0.6-0.7	4397
0.7-0.8	670
0.8-0.85	117
0.85-0.9	55
0.9-0.95	46
0.95-1	21

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC73492
0.9704	High Similarity	NPC281581
0.9647	High Similarity	NPC473716
0.9647	High Similarity	NPC475597
0.9591	High Similarity	NPC24260
0.9573	High Similarity	NPC10908
0.9573	High Similarity	NPC317439
0.9573	High Similarity	NPC63646
0.9573	High Similarity	NPC276890
0.9573	High Similarity	NPC227060
0.9573	High Similarity	NPC198498
0.9573	High Similarity	NPC76682
0.9573	High Similarity	NPC317145
0.9573	High Similarity	NPC115284
0.9515	High Similarity	NPC41376
0.9515	High Similarity	NPC12424
0.9515	High Similarity	NPC129518
0.9515	High Similarity	NPC251580
0.9401	High Similarity	NPC293093
0.929	High Similarity	NPC243454
0.929	High Similarity	NPC475479
0.9266	High Similarity	NPC475654
0.9235	High Similarity	NPC239584
0.9181	High Similarity	NPC15414
0.9181	High Similarity	NPC290582
0.9181	High Similarity	NPC290005
0.9181	High Similarity	NPC251735
0.9181	High Similarity	NPC222661
0.9181	High Similarity	NPC182052
0.9181	High Similarity	NPC258657
0.9181	High Similarity	NPC311973
0.9181	High Similarity	NPC185639
0.9181	High Similarity	NPC181796
0.9181	High Similarity	NPC223690
0.9181	High Similarity	NPC285931
0.9181	High Similarity	NPC49075
0.9181	High Similarity	NPC328155
0.9181	High Similarity	NPC271013
0.9181	High Similarity	NPC217748
0.9181	High Similarity	NPC90998
0.9181	High Similarity	NPC42663
0.9181	High Similarity	NPC7715
0.9181	High Similarity	NPC279228
0.9181	High Similarity	NPC54654
0.9181	High Similarity	NPC239824
0.9181	High Similarity	NPC104196
0.9181	High Similarity	NPC8836
0.9181	High Similarity	NPC229373
0.9128	High Similarity	NPC254441
0.9128	High Similarity	NPC167116
0.9128	High Similarity	NPC274716
0.9123	High Similarity	NPC286119
0.9075	High Similarity	NPC16357
0.9075	High Similarity	NPC302245
0.9075	High Similarity	NPC95426
0.907	High Similarity	NPC30779
0.9023	High Similarity	NPC212237
0.9023	High Similarity	NPC139783
0.9023	High Similarity	NPC116465
0.9023	High Similarity	NPC65312
0.9017	High Similarity	NPC302275
0.8971	High Similarity	NPC275680
0.8971	High Similarity	NPC22115
0.8966	High Similarity	NPC249996
0.892	High Similarity	NPC11296
0.892	High Similarity	NPC274661
0.892	High Similarity	NPC175890
0.892	High Similarity	NPC48490
0.892	High Similarity	NPC82457
0.892	High Similarity	NPC206900
0.8902	High Similarity	NPC247639
0.8902	High Similarity	NPC195538
0.8902	High Similarity	NPC25084
0.887	High Similarity	NPC191132
0.887	High Similarity	NPC60295
0.8851	High Similarity	NPC476202
0.8841	High Similarity	NPC138487
0.8841	High Similarity	NPC216459
0.8841	High Similarity	NPC41178
0.8807	High Similarity	NPC47077
0.8807	High Similarity	NPC14507
0.8788	High Similarity	NPC146288
0.8772	High Similarity	NPC19520
0.8772	High Similarity	NPC149090
0.8771	High Similarity	NPC256124
0.8715	High Similarity	NPC478093
0.8675	High Similarity	NPC234392
0.8675	High Similarity	NPC31311
0.8667	High Similarity	NPC478091
0.8667	High Similarity	NPC473589
0.8667	High Similarity	NPC478092
0.8667	High Similarity	NPC30182
0.8663	High Similarity	NPC10871
0.8639	High Similarity	NPC475393
0.8605	High Similarity	NPC75958
0.8564	High Similarity	NPC85381
0.8556	High Similarity	NPC41122
0.8556	High Similarity	NPC318805
0.8538	High Similarity	NPC476432
0.8538	High Similarity	NPC13916
0.8538	High Similarity	NPC268503
0.8538	High Similarity	NPC256012
0.8538	High Similarity	NPC250846
0.8538	High Similarity	NPC264850
0.8538	High Similarity	NPC42549
0.8538	High Similarity	NPC24264
0.8538	High Similarity	NPC240841
0.8538	High Similarity	NPC317272
0.8506	High Similarity	NPC2314
0.8494	Intermediate Similarity	NPC210148
0.8494	Intermediate Similarity	NPC233029
0.8488	Intermediate Similarity	NPC247389
0.848	Intermediate Similarity	NPC276944
0.848	Intermediate Similarity	NPC16805
0.848	Intermediate Similarity	NPC302527
0.848	Intermediate Similarity	NPC232514
0.848	Intermediate Similarity	NPC24465
0.848	Intermediate Similarity	NPC238530
0.848	Intermediate Similarity	NPC225774
0.848	Intermediate Similarity	NPC167546
0.8476	Intermediate Similarity	NPC475959
0.8476	Intermediate Similarity	NPC59907
0.8476	Intermediate Similarity	NPC37144
0.8475	Intermediate Similarity	NPC474506
0.8475	Intermediate Similarity	NPC32413
0.847	Intermediate Similarity	NPC234318
0.8466	Intermediate Similarity	NPC23219
0.8439	Intermediate Similarity	NPC83198
0.8439	Intermediate Similarity	NPC204908
0.843	Intermediate Similarity	NPC219341
0.8418	Intermediate Similarity	NPC470879
0.8418	Intermediate Similarity	NPC258695
0.8415	Intermediate Similarity	NPC210437
0.8415	Intermediate Similarity	NPC51957
0.8415	Intermediate Similarity	NPC16107
0.8415	Intermediate Similarity	NPC476144
0.8415	Intermediate Similarity	NPC106295
0.8409	Intermediate Similarity	NPC112575
0.8396	Intermediate Similarity	NPC254581
0.8382	Intermediate Similarity	NPC210918
0.8364	Intermediate Similarity	NPC7467
0.8361	Intermediate Similarity	NPC471113
0.8315	Intermediate Similarity	NPC244554
0.8304	Intermediate Similarity	NPC266753
0.8304	Intermediate Similarity	NPC477559
0.8304	Intermediate Similarity	NPC160298
0.8304	Intermediate Similarity	NPC232924
0.8304	Intermediate Similarity	NPC306902
0.8295	Intermediate Similarity	NPC232386
0.8295	Intermediate Similarity	NPC152680
0.8295	Intermediate Similarity	NPC190783
0.8287	Intermediate Similarity	NPC214116
0.8284	Intermediate Similarity	NPC93593
0.8284	Intermediate Similarity	NPC123323
0.8266	Intermediate Similarity	NPC180306
0.8258	Intermediate Similarity	NPC294790
0.8258	Intermediate Similarity	NPC118633
0.8258	Intermediate Similarity	NPC148693
0.8246	Intermediate Similarity	NPC477080
0.8246	Intermediate Similarity	NPC111485
0.8239	Intermediate Similarity	NPC475215
0.8239	Intermediate Similarity	NPC65403
0.8239	Intermediate Similarity	NPC108434
0.8197	Intermediate Similarity	NPC82763
0.8187	Intermediate Similarity	NPC57036
0.8182	Intermediate Similarity	NPC6152
0.8176	Intermediate Similarity	NPC244112
0.8171	Intermediate Similarity	NPC136860
0.8171	Intermediate Similarity	NPC476567
0.8171	Intermediate Similarity	NPC128019
0.8156	Intermediate Similarity	NPC320223
0.8156	Intermediate Similarity	NPC114364
0.8146	Intermediate Similarity	NPC199465
0.8146	Intermediate Similarity	NPC229166
0.8146	Intermediate Similarity	NPC49353
0.8146	Intermediate Similarity	NPC128560
0.8142	Intermediate Similarity	NPC186546
0.8142	Intermediate Similarity	NPC476576
0.8132	Intermediate Similarity	NPC9867
0.8081	Intermediate Similarity	NPC476572
0.807	Intermediate Similarity	NPC276588
0.807	Intermediate Similarity	NPC249797
0.807	Intermediate Similarity	NPC127674
0.807	Intermediate Similarity	NPC189266
0.807	Intermediate Similarity	NPC295691
0.807	Intermediate Similarity	NPC207757
0.807	Intermediate Similarity	NPC54379
0.807	Intermediate Similarity	NPC184026
0.807	Intermediate Similarity	NPC5238
0.807	Intermediate Similarity	NPC278799
0.807	Intermediate Similarity	NPC204828
0.807	Intermediate Similarity	NPC172765
0.807	Intermediate Similarity	NPC325871
0.807	Intermediate Similarity	NPC469817
0.807	Intermediate Similarity	NPC39701
0.807	Intermediate Similarity	NPC99659
0.807	Intermediate Similarity	NPC110416
0.807	Intermediate Similarity	NPC193949
0.807	Intermediate Similarity	NPC2413
0.8068	Intermediate Similarity	NPC298979

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 NPC299990 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	234
0.1-0.2	811
0.2-0.3	1130
0.3-0.4	2428
0.4-0.5	2413
0.5-0.6	1523
0.6-0.7	497
0.7-0.8	104
0.8-0.85	3
0.85-0.9	1
0.9-0.95	3
0.95-1	3

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9573	High Similarity	NPD8251	Approved
0.9573	High Similarity	NPD8252	Approved
0.9573	High Similarity	NPD8099	Discontinued
0.9515	High Similarity	NPD8156	Discontinued
0.9181	High Similarity	NPD8054	Approved
0.9181	High Similarity	NPD8053	Approved
0.8579	High Similarity	NPD8095	Phase 1
0.8415	Intermediate Similarity	NPD4584	Approved
0.8353	Intermediate Similarity	NPD6788	Approved
0.8049	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.7965	Intermediate Similarity	NPD7298	Approved
0.7912	Intermediate Similarity	NPD8453	Clinical (unspecified phase)
0.7895	Intermediate Similarity	NPD7261	Clinical (unspecified phase)
0.7865	Intermediate Similarity	NPD5006	Approved
0.7865	Intermediate Similarity	NPD5005	Approved
0.7831	Intermediate Similarity	NPD7667	Clinical (unspecified phase)
0.7809	Intermediate Similarity	NPD6071	Discontinued
0.7803	Intermediate Similarity	NPD4772	Phase 2
0.7803	Intermediate Similarity	NPD4773	Phase 2
0.7751	Intermediate Similarity	NPD6783	Clinical (unspecified phase)
0.7722	Intermediate Similarity	NPD4481	Phase 3
0.7709	Intermediate Similarity	NPD3051	Approved
0.7701	Intermediate Similarity	NPD7906	Approved
0.7692	Intermediate Similarity	NPD5084	Clinical (unspecified phase)
0.7661	Intermediate Similarity	NPD1424	Approved
0.7656	Intermediate Similarity	NPD4420	Approved
0.7651	Intermediate Similarity	NPD6029	Clinical (unspecified phase)
0.7651	Intermediate Similarity	NPD6028	Clinical (unspecified phase)
0.7614	Intermediate Similarity	NPD6818	Clinical (unspecified phase)
0.7598	Intermediate Similarity	NPD5677	Discontinued
0.7588	Intermediate Similarity	NPD5307	Clinical (unspecified phase)
0.7584	Intermediate Similarity	NPD7831	Phase 2
0.7584	Intermediate Similarity	NPD7833	Phase 2
0.7584	Intermediate Similarity	NPD7832	Clinical (unspecified phase)
0.7572	Intermediate Similarity	NPD6030	Approved
0.7572	Intermediate Similarity	NPD6031	Approved
0.7571	Intermediate Similarity	NPD2563	Approved
0.7571	Intermediate Similarity	NPD2560	Approved
0.7569	Intermediate Similarity	NPD2969	Approved
0.7569	Intermediate Similarity	NPD2970	Approved
0.7556	Intermediate Similarity	NPD6107	Approved
0.7544	Intermediate Similarity	NPD7124	Phase 2
0.75	Intermediate Similarity	NPD7201	Clinical (unspecified phase)
0.7487	Intermediate Similarity	NPD7310	Approved
0.7487	Intermediate Similarity	NPD7311	Approved
0.7487	Intermediate Similarity	NPD7312	Approved
0.7487	Intermediate Similarity	NPD7313	Approved
0.7486	Intermediate Similarity	NPD4017	Approved
0.7471	Intermediate Similarity	NPD3640	Phase 3
0.7471	Intermediate Similarity	NPD3639	Approved
0.7471	Intermediate Similarity	NPD3641	Approved
0.7459	Intermediate Similarity	NPD7802	Discontinued
0.7458	Intermediate Similarity	NPD3382	Approved
0.7458	Intermediate Similarity	NPD3383	Approved
0.7458	Intermediate Similarity	NPD3384	Approved
0.7447	Intermediate Similarity	NPD7309	Approved
0.7433	Intermediate Similarity	NPD7549	Discontinued
0.7432	Intermediate Similarity	NPD2489	Approved
0.7432	Intermediate Similarity	NPD27	Approved
0.7427	Intermediate Similarity	NPD7466	Approved
0.7394	Intermediate Similarity	NPD4577	Approved
0.7394	Intermediate Similarity	NPD4578	Approved
0.7389	Intermediate Similarity	NPD4055	Discovery
0.7368	Intermediate Similarity	NPD4663	Approved
0.7356	Intermediate Similarity	NPD7447	Phase 1
0.7354	Intermediate Similarity	NPD7090	Clinical (unspecified phase)
0.7349	Intermediate Similarity	NPD4475	Approved
0.7349	Intermediate Similarity	NPD4474	Approved
0.7326	Intermediate Similarity	NPD6748	Discontinued
0.7326	Intermediate Similarity	NPD6996	Clinical (unspecified phase)
0.7312	Intermediate Similarity	NPD5312	Approved
0.7312	Intermediate Similarity	NPD5313	Approved
0.7302	Intermediate Similarity	NPD2968	Approved
0.7302	Intermediate Similarity	NPD2971	Approved
0.7299	Intermediate Similarity	NPD7598	Phase 2
0.7293	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.7289	Intermediate Similarity	NPD5718	Phase 2
0.7288	Intermediate Similarity	NPD8158	Clinical (unspecified phase)
0.7278	Intermediate Similarity	NPD2200	Suspended
0.7273	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7263	Intermediate Similarity	NPD7945	Clinical (unspecified phase)
0.7252	Intermediate Similarity	NPD8153	Approved
0.7252	Intermediate Similarity	NPD8152	Approved
0.7228	Intermediate Similarity	NPD4166	Phase 2
0.7211	Intermediate Similarity	NPD7280	Phase 3
0.7211	Intermediate Similarity	NPD7281	Phase 3
0.7209	Intermediate Similarity	NPD7045	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD3124	Discontinued
0.72	Intermediate Similarity	NPD7213	Phase 3
0.72	Intermediate Similarity	NPD7212	Phase 2
0.7172	Intermediate Similarity	NPD7237	Clinical (unspecified phase)
0.7171	Intermediate Similarity	NPD7827	Phase 1
0.7159	Intermediate Similarity	NPD1754	Clinical (unspecified phase)
0.7157	Intermediate Similarity	NPD2973	Approved
0.7157	Intermediate Similarity	NPD2975	Approved
0.7157	Intermediate Similarity	NPD6621	Clinical (unspecified phase)
0.7157	Intermediate Similarity	NPD2974	Approved
0.7151	Intermediate Similarity	NPD4678	Approved
0.7151	Intermediate Similarity	NPD4675	Approved
0.713	Intermediate Similarity	NPD6625	Approved
0.7127	Intermediate Similarity	NPD5772	Approved
0.7127	Intermediate Similarity	NPD5773	Approved
0.7126	Intermediate Similarity	NPD2669	Clinical (unspecified phase)
0.7104	Intermediate Similarity	NPD5604	Discontinued
0.7095	Intermediate Similarity	NPD4005	Discontinued
0.7086	Intermediate Similarity	NPD5241	Discontinued
0.7079	Intermediate Similarity	NPD5976	Discontinued
0.7076	Intermediate Similarity	NPD6896	Approved
0.7076	Intermediate Similarity	NPD6895	Approved
0.7076	Intermediate Similarity	NPD6111	Discontinued
0.7059	Intermediate Similarity	NPD2898	Approved
0.705	Intermediate Similarity	NPD4580	Approved
0.7049	Intermediate Similarity	NPD4581	Clinical (unspecified phase)
0.7048	Intermediate Similarity	NPD8318	Clinical (unspecified phase)
0.7043	Intermediate Similarity	NPD4010	Discontinued
0.7041	Intermediate Similarity	NPD554	Clinical (unspecified phase)
0.7039	Intermediate Similarity	NPD4210	Discontinued
0.7033	Intermediate Similarity	NPD4585	Approved
0.7033	Intermediate Similarity	NPD2977	Approved
0.7033	Intermediate Similarity	NPD2978	Approved
0.7022	Intermediate Similarity	NPD3647	Clinical (unspecified phase)
0.7015	Intermediate Similarity	NPD3450	Approved
0.7015	Intermediate Similarity	NPD3452	Approved
0.7015	Intermediate Similarity	NPD2493	Approved
0.7015	Intermediate Similarity	NPD2494	Approved
0.7009	Intermediate Similarity	NPD7224	Discontinued
0.7009	Intermediate Similarity	NPD7223	Discontinued
0.7005	Intermediate Similarity	NPD3815	Phase 1
0.7005	Intermediate Similarity	NPD3816	Phase 1
0.7	Intermediate Similarity	NPD3885	Approved
0.6995	Remote Similarity	NPD6851	Approved
0.6995	Remote Similarity	NPD6853	Approved
0.699	Remote Similarity	NPD2488	Approved
0.699	Remote Similarity	NPD2490	Approved
0.6977	Remote Similarity	NPD7119	Phase 2
0.6974	Remote Similarity	NPD7291	Discontinued
0.6974	Remote Similarity	NPD6842	Approved
0.6974	Remote Similarity	NPD6841	Approved
0.6974	Remote Similarity	NPD6843	Phase 3
0.6971	Remote Similarity	NPD4237	Approved
0.6971	Remote Similarity	NPD4236	Phase 3
0.6965	Remote Similarity	NPD5457	Discontinued
0.6963	Remote Similarity	NPD6297	Approved
0.6948	Remote Similarity	NPD6997	Phase 2
0.6946	Remote Similarity	NPD7247	Discontinued
0.6939	Remote Similarity	NPD7235	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD5582	Discontinued
0.6932	Remote Similarity	NPD5754	Discontinued
0.6932	Remote Similarity	NPD6658	Clinical (unspecified phase)
0.6931	Remote Similarity	NPD5602	Clinical (unspecified phase)
0.6915	Remote Similarity	NPD5242	Approved
0.6912	Remote Similarity	NPD4582	Approved
0.6912	Remote Similarity	NPD4583	Approved
0.691	Remote Similarity	NPD2420	Approved
0.691	Remote Similarity	NPD2421	Approved
0.691	Remote Similarity	NPD5297	Approved
0.6906	Remote Similarity	NPD6523	Clinical (unspecified phase)
0.6905	Remote Similarity	NPD7047	Phase 3
0.6898	Remote Similarity	NPD7199	Phase 2
0.6895	Remote Similarity	NPD6723	Discontinued
0.6891	Remote Similarity	NPD7132	Clinical (unspecified phase)
0.6889	Remote Similarity	NPD2122	Discontinued
0.6888	Remote Similarity	NPD7243	Clinical (unspecified phase)
0.6882	Remote Similarity	NPD6812	Clinical (unspecified phase)
0.6878	Remote Similarity	NPD7607	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD5177	Phase 3
0.6872	Remote Similarity	NPD5087	Clinical (unspecified phase)
0.6872	Remote Similarity	NPD4123	Phase 3
0.6863	Remote Similarity	NPD4004	Approved
0.6863	Remote Similarity	NPD4002	Approved
0.6857	Remote Similarity	NPD1375	Discontinued
0.6834	Remote Similarity	NPD7125	Discontinued
0.6831	Remote Similarity	NPD5090	Approved
0.6831	Remote Similarity	NPD7110	Phase 1
0.6831	Remote Similarity	NPD5089	Approved
0.6831	Remote Similarity	NPD6072	Discontinued
0.6831	Remote Similarity	NPD7109	Clinical (unspecified phase)
0.6826	Remote Similarity	NPD7258	Clinical (unspecified phase)
0.6825	Remote Similarity	NPD8051	Clinical (unspecified phase)
0.6825	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6821	Remote Similarity	NPD2492	Phase 1
0.6821	Remote Similarity	NPD6618	Phase 2
0.6818	Remote Similarity	NPD5525	Clinical (unspecified phase)
0.6816	Remote Similarity	NPD7837	Clinical (unspecified phase)
0.6814	Remote Similarity	NPD7590	Clinical (unspecified phase)
0.6811	Remote Similarity	NPD5977	Approved
0.6811	Remote Similarity	NPD5978	Approved
0.6806	Remote Similarity	NPD4498	Clinical (unspecified phase)
0.6802	Remote Similarity	NPD3110	Approved
0.6802	Remote Similarity	NPD3109	Approved
0.68	Remote Similarity	NPD6493	Phase 3
0.6798	Remote Similarity	NPD7501	Clinical (unspecified phase)
0.6796	Remote Similarity	NPD4727	Phase 1
0.6793	Remote Similarity	NPD5720	Discontinued
0.6788	Remote Similarity	NPD7007	Discovery
0.6784	Remote Similarity	NPD7296	Approved
0.678	Remote Similarity	NPD4162	Approved
0.676	Remote Similarity	NPD6666	Approved
0.676	Remote Similarity	NPD3845	Phase 1
0.676	Remote Similarity	NPD6667	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