NPASS Compound

Natural Product: NPC608788

Natural Product ID	NPC608788
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BGOFCVIGEYGEOF-UJPOAAIJSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2289230
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 36 37 0 0 0 0 0 0 0 0999 V2000 4.0883 2.7349 1.8368 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1166 2.0634 1.4268 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3292 1.0198 0.4153 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5908 0.7900 -0.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8213 -0.1886 -1.0267 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7580 -0.9394 -1.4900 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4935 -0.6997 -0.9935 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2453 0.2629 -0.0492 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0183 0.5540 0.4867 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1718 -0.0767 0.1619 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0481 0.8920 -0.3348 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2303 0.3116 -0.8244 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0015 1.3839 -1.5571 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1859 0.9300 -2.0834 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9708 -0.2524 0.3451 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2352 -0.7179 0.0288 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0936 -1.3617 0.9251 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7175 -2.0715 1.9133 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8272 -0.6548 1.4250 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0339 -1.5949 2.0341 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1245 2.2521 1.8168 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4368 1.3674 0.2787 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8180 -0.3873 -1.4271 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8785 -1.7186 -2.2370 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6815 -1.2939 -1.3667 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1275 -0.8722 -0.5833 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9671 -0.5205 -1.5064 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3533 1.6812 -2.4311 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0937 2.2996 -0.9446 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7967 1.7235 -2.1668 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0699 0.4989 1.1748 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4383 -1.4565 0.6586 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7532 -1.9862 0.0633 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9063 -2.9942 1.5514 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1339 0.1657 2.0958 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7553 -1.1441 2.4554 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 8 3 1 0 19 10 1 0 2 21 1 0 4 22 1 0 5 23 1 0 6 24 1 0 7 25 1 0 10 26 1 6 12 27 1 6 13 28 1 0 13 29 1 0 14 30 1 0 15 31 1 1 16 32 1 0 17 33 1 6 18 34 1 0 19 35 1 1 20 36 1 0 M END

Standard InCHIKey	BGOFCVIGEYGEOF-UJPOAAIJSA-N
Standard InCHI	InChI=1S/C13H16O7/c14-5-7-3-1-2-4-8(7)19-13-12(18)11(17)10(16)9(6-15)20-13/h1-5,9-13,15-18H,6H2/t9-,10-,11+,12-,13-/m1/s1
SMILES	O=Cc1ccccc1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO19899	Crepis foetida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19899	Crepis foetida	Species	Asteraceae	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	Organism Name	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
Activity	3
EC50	4
EC100	1

Activity Type	# Activity
Organism	4
Single protein	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT27193	Single protein	Taste receptor type 2 member 16	Homo sapiens	Activity	=	0.3	mM	EP-2267129-B1
NPT27193	Single protein	Taste receptor type 2 member 16	Homo sapiens	EC50	=	2300000.0	nM	EP-2267129-B1

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT450	Organism	Meloidogyne incognita	Meloidogyne incognita	EC100	>	250.0	mg/L	PMID[23379671]
NPT450	Organism	Meloidogyne incognita	Meloidogyne incognita	EC50	>	250.0	ug.mL-1	PMID[23379671]
NPT605	Organism	Homo sapiens	Homo sapiens	Activity	=	0.4	mM	EP-2267129-B1
NPT605	Organism	Homo sapiens	Homo sapiens	EC50	=	2200000.0	nM	EP-2267129-B1

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC608788 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	17407
0.1-0.2	28477
0.2-0.3	2970
0.3-0.4	656
0.4-0.5	255
0.5-0.6	72
0.6-0.7	7
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.75	Intermediate Similarity	NPC226712
0.6809	Remote Similarity	NPC212729
0.6809	Remote Similarity	NPC604498
0.6667	Remote Similarity	NPC228907
0.6316	Remote Similarity	NPC34456
0.6207	Remote Similarity	NPC146540
0.6207	Remote Similarity	NPC269421
0.6	Remote Similarity	NPC269242
0.5962	Remote Similarity	NPC299144
0.5882	Remote Similarity	NPC294470
0.5818	Remote Similarity	NPC215833
0.5789	Remote Similarity	NPC164599
0.5769	Remote Similarity	NPC9248
0.5741	Remote Similarity	NPC69513
0.5738	Remote Similarity	NPC610808
0.5714	Remote Similarity	NPC218685
0.5686	Remote Similarity	NPC217854
0.566	Remote Similarity	NPC60589
0.566	Remote Similarity	NPC469708
0.566	Remote Similarity	NPC609376
0.5636	Remote Similarity	NPC48863
0.5636	Remote Similarity	NPC166040
0.5636	Remote Similarity	NPC251981
0.5636	Remote Similarity	NPC13745
0.5614	Remote Similarity	NPC606892
0.5593	Remote Similarity	NPC222455
0.5574	Remote Similarity	NPC134260
0.5556	Remote Similarity	NPC200092
0.5556	Remote Similarity	NPC302989
0.5536	Remote Similarity	NPC40377
0.5536	Remote Similarity	NPC9912
0.5517	Remote Similarity	NPC210478
0.549	Remote Similarity	NPC276195
0.549	Remote Similarity	NPC142319
0.5472	Remote Similarity	NPC152722
0.5455	Remote Similarity	NPC80098
0.5439	Remote Similarity	NPC49074
0.5424	Remote Similarity	NPC479029
0.5397	Remote Similarity	NPC600107
0.5373	Remote Similarity	NPC217950
0.5357	Remote Similarity	NPC166168
0.5345	Remote Similarity	NPC472024
0.5345	Remote Similarity	NPC162093
0.5345	Remote Similarity	NPC479028
0.5345	Remote Similarity	NPC270849
0.5345	Remote Similarity	NPC205054
0.5345	Remote Similarity	NPC479031
0.5345	Remote Similarity	NPC602619
0.5283	Remote Similarity	NPC153149
0.5273	Remote Similarity	NPC12308
0.5254	Remote Similarity	NPC26653
0.5254	Remote Similarity	NPC80600
0.5246	Remote Similarity	NPC218003
0.5238	Remote Similarity	NPC479030
0.5217	Remote Similarity	NPC166180
0.5185	Remote Similarity	NPC25817
0.5167	Remote Similarity	NPC248355
0.5152	Remote Similarity	NPC278329
0.5152	Remote Similarity	NPC92054
0.5152	Remote Similarity	NPC146837
0.5143	Remote Similarity	NPC292443
0.5139	Remote Similarity	NPC199928
0.5094	Remote Similarity	NPC484157
0.5091	Remote Similarity	NPC604439
0.5088	Remote Similarity	NPC214454
0.5088	Remote Similarity	NPC95292
0.5085	Remote Similarity	NPC251102
0.5085	Remote Similarity	NPC485268
0.5085	Remote Similarity	NPC210298
0.5085	Remote Similarity	NPC23084
0.5085	Remote Similarity	NPC19470
0.5085	Remote Similarity	NPC604356
0.5082	Remote Similarity	NPC95392
0.5082	Remote Similarity	NPC84013
0.5082	Remote Similarity	NPC55715
0.5082	Remote Similarity	NPC106025
0.5082	Remote Similarity	NPC55040
0.5082	Remote Similarity	NPC35877
0.5077	Remote Similarity	NPC210192
0.5075	Remote Similarity	NPC101116

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC608788 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3463
0.1-0.2	5425
0.2-0.3	237
0.3-0.4	21
0.4-0.5	3
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.75	Intermediate Similarity	NPD1091	Pre-clinical

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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