NPASS Compound

Natural Product: NPC320825

Natural Product ID	NPC320825
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Tamaraxetin
IUPAC Name	3,5,7-trihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydrochromen-4-one
Synonyms	Dihydrotamarixetin
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL451709
PubChem CID	482576
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002596] 4'-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 5.9590 0.1884 1.0977 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3032 0.1065 -0.1422 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9115 -0.0687 -0.2343 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2738 -0.1483 -1.4451 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9006 -0.3212 -1.5128 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1163 -0.4206 -0.3829 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7768 -0.3380 0.8263 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1485 -0.1654 0.9096 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3353 -0.6029 -0.4118 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9786 -0.5033 -1.7352 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4690 -0.4790 -1.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1977 -0.8079 -2.4926 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0656 -0.1008 -0.2650 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4418 -0.1158 -0.0585 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9474 0.2589 1.1682 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1415 0.6524 2.2115 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7877 0.6674 2.0089 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2491 0.2931 0.7773 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8916 0.3008 0.5519 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7040 1.0243 3.4400 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2874 -0.5073 -1.0882 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6657 0.5974 -2.4844 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0017 -0.0560 -2.6226 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0966 -0.8308 1.5415 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9994 0.5509 0.8947 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4574 0.8439 1.8270 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4583 -0.3765 -2.4792 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2253 -0.4080 1.7683 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6498 -0.1028 1.8805 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5550 -1.6244 -0.0089 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7878 -1.4236 -2.3245 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0291 0.2589 1.3664 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1357 0.9706 2.8070 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1068 1.5740 4.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5185 0.2086 -1.7771 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8423 0.4265 -3.4496 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8596 0.4785 -2.7118 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 6 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 16 20 1 0 14 21 1 0 10 22 1 0 4 23 1 0 8 3 1 0 19 9 1 0 18 13 1 0 1 24 1 0 1 25 1 0 1 26 1 0 5 27 1 0 7 28 1 0 8 29 1 0 9 30 1 0 10 31 1 0 15 32 1 0 17 33 1 0 20 34 1 0 21 35 1 0 22 36 1 0 23 37 1 0 M END

Standard InCHIKey	KQNGHARGJDXHKF-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C16H14O7/c1-22-11-3-2-7(4-9(11)18)16-15(21)14(20)13-10(19)5-8(17)6-12(13)23-16/h2-6,15-19,21H,1H3
SMILES	COC1=C(C=C(C=C1)C2C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O

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
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787457]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	leaf	n.a.	PMID[21319848]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32544201]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21559	Blumea balsamifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21559	Blumea balsamifera	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
IC50	1
EC50	1

Activity Type	# Activity
Others	2

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
NPT1	Others	Radical scavenging activity	n.a.	EC50	>	100.0	ug	PMID[21821414]
NPT2	Others	Unspecified	n.a.	IC50	=	70000.0	nM	PMID[10096854]

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 NPC320825 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	24254
0.1-0.2	20527
0.2-0.3	4436
0.3-0.4	474
0.4-0.5	99
0.5-0.6	21
0.6-0.7	21
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	Natural Product ID
0.8039	Intermediate Similarity	NPC250922
0.7843	Intermediate Similarity	NPC44721
0.7843	Intermediate Similarity	NPC211466
0.7843	Intermediate Similarity	NPC605332
0.7455	Intermediate Similarity	NPC326037
0.7455	Intermediate Similarity	NPC13858
0.7358	Intermediate Similarity	NPC36835
0.7358	Intermediate Similarity	NPC246162
0.7358	Intermediate Similarity	NPC9743
0.7358	Intermediate Similarity	NPC260491
0.7358	Intermediate Similarity	NPC61506
0.7358	Intermediate Similarity	NPC240476
0.7255	Intermediate Similarity	NPC21835
0.7115	Intermediate Similarity	NPC62290
0.7115	Intermediate Similarity	NPC142731
0.7115	Intermediate Similarity	NPC326506
0.7115	Intermediate Similarity	NPC4152
0.6981	Remote Similarity	NPC19721
0.6522	Remote Similarity	NPC75827
0.6491	Remote Similarity	NPC471515
0.6481	Remote Similarity	NPC279417
0.6481	Remote Similarity	NPC49130
0.6316	Remote Similarity	NPC302950
0.625	Remote Similarity	NPC306607
0.625	Remote Similarity	NPC606962
0.6232	Remote Similarity	NPC138688
0.6232	Remote Similarity	NPC72787
0.6232	Remote Similarity	NPC217795
0.6232	Remote Similarity	NPC58223
0.6182	Remote Similarity	NPC208176
0.6143	Remote Similarity	NPC279209
0.6143	Remote Similarity	NPC102277
0.6143	Remote Similarity	NPC479117
0.6087	Remote Similarity	NPC36916
0.6087	Remote Similarity	NPC36
0.6087	Remote Similarity	NPC7154
0.6087	Remote Similarity	NPC125039
0.6087	Remote Similarity	NPC7688
0.5862	Remote Similarity	NPC609065
0.5797	Remote Similarity	NPC606364
0.569	Remote Similarity	NPC176869
0.569	Remote Similarity	NPC3779
0.5556	Remote Similarity	NPC282009
0.5517	Remote Similarity	NPC122828
0.5424	Remote Similarity	NPC263449
0.541	Remote Similarity	NPC52530
0.5254	Remote Similarity	NPC246328
0.5254	Remote Similarity	NPC27532
0.5246	Remote Similarity	NPC611035
0.5172	Remote Similarity	NPC476182
0.5167	Remote Similarity	NPC308992
0.5167	Remote Similarity	NPC481903
0.5139	Remote Similarity	NPC186847
0.5088	Remote Similarity	NPC1940
0.5085	Remote Similarity	NPC47398
0.5085	Remote Similarity	NPC234333
0.5085	Remote Similarity	NPC260898
0.5082	Remote Similarity	NPC260979
0.5082	Remote Similarity	NPC61946

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC320825 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4524
0.1-0.2	4507
0.2-0.3	106
0.3-0.4	5
0.4-0.5	4
0.5-0.6	0
0.6-0.7	4
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
0.6316	Remote Similarity	NPD1934	Phase 0
0.6087	Remote Similarity	NPD6166	Phase 2
0.6087	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6087	Remote Similarity	NPD6168	Clinical (unspecified phase)

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