NPASS Compound

Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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

Natural Product: NPC316435

*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

☑ 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
LD50	1
MIC	10
Others	1
Potency	53

Activity Type	# Activity
Cell Line	1
Individual Protein	15
Organism	13
Others	36

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT56	Individual Protein	Beta-lactamase AmpC	Escherichia coli K-12	Potency	=	1778.3	nM	PMID[506150]
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	50118.7	nM	PMID[506151]
NPT249	Individual Protein	Glucocorticoid receptor	Homo sapiens	Potency	n.a.	50118.7	nM	PMID[506149]
NPT65	Cell Line	HepG2	Homo sapiens	Potency	n.a.	15848.9	nM	PMID[506150]
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	14125.4	nM	PMID[506149]
NPT154	Individual Protein	Mothers against decapentaplegic homolog 3	Homo sapiens	Potency	n.a.	25118.9	nM	PMID[506150]
NPT539	Individual Protein	Cellular tumor antigen p53	Homo sapiens	Potency	n.a.	8912.5	nM	PMID[506149]
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	74978.0	nM	PMID[506149]
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	61130.6	nM	PMID[506151]
NPT11	Individual Protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency	n.a.	8912.5	nM	PMID[506150]
NPT158	Individual Protein	Nuclear receptor subfamily 1 group I member 2	Rattus norvegicus	Potency	n.a.	100000.0	nM	PMID[506151]
NPT103	Individual Protein	Nuclear receptor ROR-gamma	Homo sapiens	Potency	n.a.	26603.2	nM	PMID[506149]
NPT160	Individual Protein	TAR DNA-binding protein 43	Homo sapiens	Potency	n.a.	3162.3	nM	PMID[506150]
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	17373.9	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	61130.6	nM	PubChem BioAssay data set
NPT851	Organism	Colletotrichum fragariae	Colletotrichum fragariae	IZ	=	80.0	mm	PMID[506147]
NPT94	Individual Protein	Aldehyde dehydrogenase 1A1	Homo sapiens	Potency	=	39810.7	nM	PMID[506149]
NPT2	Others	Unspecified		Potency	=	8199.5	nM	PMID[506150]
NPT2	Others	Unspecified		Potency	n.a.	20596.2	nM	PMID[506150]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	18526.0	nM	PMID[506150]
NPT2	Others	Unspecified		Potency	n.a.	42163.2	nM	PMID[506149]
NPT2	Others	Unspecified		Potency	n.a.	29849.3	nM	PMID[506149]
NPT32	Organism	Mus musculus	Mus musculus	LD50	=	1500.0	mg.kg-1	PMID[506152]
NPT635	Organism	Botryotinia fuckeliana	Botryotinia fuckeliana	MIC	=	0.1	ug.mL-1	PMID[506152]
NPT5960	Organism	Penicillium brevicompactum	Penicillium brevicompactum	MIC	>	25.0	ug.mL-1	PMID[506153]
NPT5960	Organism	Penicillium brevicompactum	Penicillium brevicompactum	MIC	=	25.0	ug.mL-1	PMID[506153]
NPT5960	Organism	Penicillium brevicompactum	Penicillium brevicompactum	MIC	=	12.5	ug.mL-1	PMID[506153]
NPT1262	Organism	Aspergillus parasiticus	Aspergillus parasiticus	MIC	>	25.0	ug.mL-1	PMID[506153]
NPT635	Organism	Botryotinia fuckeliana	Botryotinia fuckeliana	MIC	=	6.25	ug.mL-1	PMID[506153]
NPT635	Organism	Botryotinia fuckeliana	Botryotinia fuckeliana	MIC	=	3.12	ug.mL-1	PMID[506153]
NPT2	Others	Unspecified		Potency	n.a.	55310.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	6916.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	6164.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	34376.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	4364.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	24485.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	1548.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	4327.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	2753.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	5.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	54482.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	61130.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	7695.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	21872.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	43935	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	24541.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	24706.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	27535.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	68589.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	2747.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	11036	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	30824.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	24336.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	9770	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	27306	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	48557.7	nM	PubChem BioAssay data set

☑ 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 NPC316435 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	3597
0.1-0.2	17013
0.2-0.3	17886
0.3-0.4	3775
0.4-0.5	362
0.5-0.6	53
0.6-0.7	9
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7857	Intermediate Similarity	NPC240134
0.6947	Remote Similarity	NPC301874
0.6702	Remote Similarity	NPC271732
0.6435	Remote Similarity	NPC313362
0.6435	Remote Similarity	NPC313810
0.6283	Remote Similarity	NPC323726
0.6262	Remote Similarity	NPC297532
0.6162	Remote Similarity	NPC66775
0.6055	Remote Similarity	NPC315403
0.6019	Remote Similarity	NPC43655
0.5943	Remote Similarity	NPC134825
0.5917	Remote Similarity	NPC44836
0.5909	Remote Similarity	NPC107135
0.5905	Remote Similarity	NPC307456
0.5873	Remote Similarity	NPC125416
0.5872	Remote Similarity	NPC262295
0.5856	Remote Similarity	NPC92689
0.5841	Remote Similarity	NPC476483
0.5833	Remote Similarity	NPC229477
0.5806	Remote Similarity	NPC119076
0.5794	Remote Similarity	NPC15839
0.5772	Remote Similarity	NPC329358
0.5766	Remote Similarity	NPC173991
0.5714	Remote Similarity	NPC191444
0.5676	Remote Similarity	NPC30445
0.5676	Remote Similarity	NPC111233
0.5669	Remote Similarity	NPC218710
0.5635	Remote Similarity	NPC322735
0.5625	Remote Similarity	NPC176858

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 NPC316435 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	636
0.1-0.2	1487
0.2-0.3	2906
0.3-0.4	3198
0.4-0.5	797
0.5-0.6	107
0.6-0.7	18
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.82	Intermediate Similarity	NPD9070	Clinical (unspecified phase)
0.6833	Remote Similarity	NPD9700	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD9475	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD190	Phase 1
0.6638	Remote Similarity	NPD916	Discontinued
0.6613	Remote Similarity	NPD9527	Approved
0.6613	Remote Similarity	NPD9528	Approved
0.6579	Remote Similarity	NPD233	Clinical (unspecified phase)
0.6565	Remote Similarity	NPD9467	Clinical (unspecified phase)
0.6535	Remote Similarity	NPD525	Clinical (unspecified phase)
0.6441	Remote Similarity	NPD909	Clinical (unspecified phase)
0.6308	Remote Similarity	NPD9701	Discontinued
0.6288	Remote Similarity	NPD1502	Approved
0.626	Remote Similarity	NPD1171	Approved
0.6148	Remote Similarity	NPD452	Phase 1
0.6148	Remote Similarity	NPD453	Phase 1
0.6129	Remote Similarity	NPD9719	Approved
0.6129	Remote Similarity	NPD9720	Approved
0.6055	Remote Similarity	NPD9108	Approved
0.6032	Remote Similarity	NPD726	Discontinued
0.6032	Remote Similarity	NPD541	Approved
0.6027	Remote Similarity	NPD1162	Approved
0.6016	Remote Similarity	NPD456	Approved
0.5984	Remote Similarity	NPD526	Approved
0.5935	Remote Similarity	NPD561	Approved
0.5935	Remote Similarity	NPD560	Approved
0.5931	Remote Similarity	NPD1204	Discontinued
0.5906	Remote Similarity	NPD9476	Approved
0.5891	Remote Similarity	NPD9252	Approved
0.5874	Remote Similarity	NPD9691	Discontinued
0.5873	Remote Similarity	NPD5243	Approved
0.5873	Remote Similarity	NPD5245	Approved
0.5873	Remote Similarity	NPD5244	Approved
0.5859	Remote Similarity	NPD9246	Approved
0.5841	Remote Similarity	NPD1394	Approved
0.5827	Remote Similarity	NPD299	Phase 3
0.5827	Remote Similarity	NPD9247	Phase 3
0.5827	Remote Similarity	NPD457	Approved
0.5802	Remote Similarity	NPD2964	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD9188	Approved
0.5766	Remote Similarity	NPD9686	Discontinued
0.5714	Remote Similarity	NPD7442	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD986	Discontinued
0.5692	Remote Similarity	NPD1525	Approved
0.569	Remote Similarity	NPD9352	Approved
0.569	Remote Similarity	NPD716	Approved
0.5643	Remote Similarity	NPD1206	Approved
0.5643	Remote Similarity	NPD1207	Approved
0.5641	Remote Similarity	NPD9304	Approved
0.5639	Remote Similarity	NPD1885	Approved
0.5615	Remote Similarity	NPD3499	Approved
0.5615	Remote Similarity	NPD3498	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