NPASS Compound

Natural Product: NPC312924

Natural Product ID	NPC312924
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ONGSIZGYZVYYNI-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002591] 6-O-methylated flavonoids

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 37 39 0 0 0 0 0 0 0 0999 V2000 -4.5537 -2.0594 -0.2602 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0613 -0.7723 -0.5102 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1577 0.2787 -0.5999 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8013 0.0973 -0.4532 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8786 1.1463 -0.5410 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4273 2.3862 -0.7869 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7926 2.6009 -0.9397 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6564 1.5409 -0.8451 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0352 1.7069 -0.9913 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4592 0.9028 -0.3789 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4479 1.9238 -0.4634 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7774 1.6297 -0.3011 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6161 2.5771 -0.3797 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1768 0.3321 -0.0591 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5206 0.0326 0.1054 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9286 -1.2525 0.3461 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9433 -2.2330 0.4173 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5964 -1.9267 0.2515 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2003 -0.6279 0.0096 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0705 -0.3425 -0.1462 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3670 -3.5243 0.6604 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2688 -1.6026 0.5183 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2188 -0.5741 0.4364 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8719 -2.3088 -1.1059 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3487 -2.8315 -0.2666 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0383 -2.0486 0.7135 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4138 -0.8899 -0.2617 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8084 3.2588 -0.8728 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2080 3.5857 -1.1333 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4188 2.4076 -1.6154 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1558 2.9411 -0.6513 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2574 0.8290 0.0420 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8499 -2.7073 0.3115 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1725 -3.6794 1.2778 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0957 0.0167 -0.5132 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1462 0.1346 1.2992 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2620 -0.9480 0.4166 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 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 5 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 17 21 1 0 16 22 1 0 22 23 1 0 8 3 1 0 20 10 1 0 19 14 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 6 28 1 0 7 29 1 0 9 30 1 0 11 31 1 0 15 32 1 0 18 33 1 0 21 34 1 0 23 35 1 0 23 36 1 0 23 37 1 0 M END

Standard InCHIKey	ONGSIZGYZVYYNI-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C17H14O6/c1-21-16-5-9(3-4-11(16)18)14-7-12(19)10-6-17(22-2)13(20)8-15(10)23-14/h3-8,18,20H,1-2H3
SMILES	COc1cc(ccc1O)c1cc(=O)c2cc(c(cc2o1)O)OC

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
NPO40372	Tephrosia linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32155073]
NPO40372	Tephrosia linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	5

Activity Type	# Activity
Cell line	5

Molecular-level activity

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

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	170.51	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	17.72	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	43.11	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	17.39	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	4.03	%	PMID[32155073]

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 NPC312924 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	30036
0.1-0.2	16333
0.2-0.3	2669
0.3-0.4	606
0.4-0.5	165
0.5-0.6	28
0.6-0.7	8
0.7-0.8	0
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
0.7778	Intermediate Similarity	NPC115323
0.7593	Intermediate Similarity	NPC20830
0.7273	Intermediate Similarity	NPC83508
0.6724	Remote Similarity	NPC183950
0.6441	Remote Similarity	NPC47781
0.6441	Remote Similarity	NPC137062
0.6441	Remote Similarity	NPC606105
0.6102	Remote Similarity	NPC280339
0.6102	Remote Similarity	NPC167815
0.6	Remote Similarity	NPC4455
0.6	Remote Similarity	NPC128863
0.5902	Remote Similarity	NPC227325
0.5821	Remote Similarity	NPC602497
0.5738	Remote Similarity	NPC602125
0.5738	Remote Similarity	NPC604422
0.5738	Remote Similarity	NPC607642
0.5593	Remote Similarity	NPC241498
0.5593	Remote Similarity	NPC284552
0.5593	Remote Similarity	NPC483774
0.55	Remote Similarity	NPC100887
0.55	Remote Similarity	NPC266597
0.5405	Remote Similarity	NPC475942
0.5323	Remote Similarity	NPC255350
0.5263	Remote Similarity	NPC606560
0.5246	Remote Similarity	NPC250266
0.5238	Remote Similarity	NPC256612
0.5238	Remote Similarity	NPC236223
0.5167	Remote Similarity	NPC293183
0.5161	Remote Similarity	NPC256283
0.5156	Remote Similarity	NPC252933
0.5156	Remote Similarity	NPC125062
0.5156	Remote Similarity	NPC279989
0.5156	Remote Similarity	NPC604021
0.5088	Remote Similarity	NPC172262
0.5082	Remote Similarity	NPC156222
0.5082	Remote Similarity	NPC47815
0.5082	Remote Similarity	NPC609062
0.5077	Remote Similarity	NPC227192
0.5077	Remote Similarity	NPC480710

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC312924 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5638
0.1-0.2	3426
0.2-0.3	80
0.3-0.4	4
0.4-0.5	1
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
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
0.5323	Remote Similarity	NPD2801	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