NPASS Compound

Natural Product: NPC85131

Natural Product ID	NPC85131
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5,7,3',4'-Tetrahydroxy-2'-(3,3-Dimethylallyl)Isoflavone
IUPAC Name	3-[3,4-dihydroxy-2-(3-methylbut-2-enyl)phenyl]-5,7-dihydroxychromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL491480
PubChem CID	11610052
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002901] Isoflav-2-enes [CHEMONTID:0000494] Isoflavones [CHEMONTID:0003580] 2'-prenylated isoflavones

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 44 46 0 0 0 0 0 0 0 0999 V2000 -3.9053 2.3642 0.1701 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3206 1.1492 -0.4317 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1181 0.7331 -0.0806 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4723 -0.4811 -0.6453 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0726 -1.4384 0.3826 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0943 -1.2995 1.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4066 -2.2489 2.0674 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4690 -3.2997 2.3095 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6450 -3.4385 1.6034 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9471 -2.5065 0.6386 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1296 -2.6618 -0.0597 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4999 -4.5211 1.8850 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0003 -0.2160 0.8052 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9844 0.9330 1.5484 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8484 1.9168 1.3007 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7457 1.8349 0.3456 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6433 2.8522 0.0851 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5892 2.7771 -0.9153 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6601 1.6339 -1.7098 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7764 0.6148 -1.4643 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8443 0.7157 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9362 -0.3161 -0.2001 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9723 -1.3576 -0.8956 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8135 -0.5342 -2.2278 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5029 3.7815 -1.2010 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0958 0.4098 -1.4472 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5587 2.0410 1.0266 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1447 3.0996 0.5092 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5909 2.8991 -0.5315 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6181 1.3556 0.6733 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1506 -0.9191 -1.4131 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5902 -0.1100 -1.2193 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3303 -2.1082 2.5965 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2193 -4.0259 3.0719 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4672 -3.5438 -0.4223 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3828 -5.4063 1.3682 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2606 1.0317 2.3397 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6032 3.7450 0.6899 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4125 1.5710 -2.5079 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4002 -1.3349 -2.0057 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4890 3.5796 -1.1163 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4755 -0.5605 -1.1193 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4518 0.3068 -2.3512 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9889 0.9824 -1.7961 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 9 12 1 0 6 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 20 24 1 0 18 25 1 0 2 26 1 0 10 5 1 0 22 13 1 0 21 16 1 0 1 27 1 0 1 28 1 0 1 29 1 0 3 30 1 0 4 31 1 0 4 32 1 0 7 33 1 0 8 34 1 0 11 35 1 0 12 36 1 0 14 37 1 0 17 38 1 0 19 39 1 0 24 40 1 0 25 41 1 0 26 42 1 0 26 43 1 0 26 44 1 0 M END

Standard InCHIKey	XIUMMQJDWWYGHD-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C20H18O6/c1-10(2)3-4-13-12(5-6-15(22)19(13)24)14-9-26-17-8-11(21)7-16(23)18(17)20(14)25/h3,5-9,21-24H,4H2,1-2H3
SMILES	CC(=CCc1c(ccc(c1O)O)c1coc2cc(cc(c2c1=O)O)O)C

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
NPO11841	Psorothamnus arborescens	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[16441066]
NPO11841	Psorothamnus arborescens	Species	Fabaceae	Eukaryota	root	n.a.	n.a.	PMID[16441066]
NPO11841	Psorothamnus arborescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11841	Psorothamnus arborescens	Species	Fabaceae	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	4

Activity Type	# Activity
Cell line	2
Organism	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
NPT189	Cell line	Vero	Chlorocebus aethiops	IC50	=	37500.0	nM	PMID[16441066]
NPT306	Cell line	PC-3	Homo sapiens	IC50	=	12700.0	nM	PMID[16441066]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	=	13000.0	nM	PMID[16441066]
NPT471	Organism	Trypanosoma brucei brucei	Trypanosoma brucei brucei	IC50	=	12100.0	nM	PMID[16441066]

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 NPC85131 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	23926
0.1-0.2	23192
0.2-0.3	2188
0.3-0.4	426
0.4-0.5	81
0.5-0.6	33
0.6-0.7	6
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
0.7705	Intermediate Similarity	NPC93552
0.6769	Remote Similarity	NPC238279
0.6667	Remote Similarity	NPC213659
0.6667	Remote Similarity	NPC326109
0.6667	Remote Similarity	NPC232947
0.6232	Remote Similarity	NPC233918
0.6	Remote Similarity	NPC268059
0.5921	Remote Similarity	NPC303174
0.5915	Remote Similarity	NPC128774
0.5915	Remote Similarity	NPC485109
0.5811	Remote Similarity	NPC474960
0.5806	Remote Similarity	NPC87545
0.5806	Remote Similarity	NPC38065
0.5738	Remote Similarity	NPC39426
0.5556	Remote Similarity	NPC475705
0.5522	Remote Similarity	NPC309154
0.5493	Remote Similarity	NPC268204
0.5484	Remote Similarity	NPC608554
0.5479	Remote Similarity	NPC56786
0.5333	Remote Similarity	NPC488567
0.5323	Remote Similarity	NPC193792
0.5301	Remote Similarity	NPC324447
0.5286	Remote Similarity	NPC259166
0.5224	Remote Similarity	NPC294409
0.5224	Remote Similarity	NPC490701
0.5217	Remote Similarity	NPC279668
0.5211	Remote Similarity	NPC20472
0.5205	Remote Similarity	NPC606200
0.5143	Remote Similarity	NPC254702
0.5143	Remote Similarity	NPC483637
0.5143	Remote Similarity	NPC476055
0.5143	Remote Similarity	NPC264550
0.5139	Remote Similarity	NPC40868
0.5132	Remote Similarity	NPC303197
0.5075	Remote Similarity	NPC78341
0.5072	Remote Similarity	NPC89474
0.5072	Remote Similarity	NPC200316
0.507	Remote Similarity	NPC144118
0.5068	Remote Similarity	NPC203077
0.5067	Remote Similarity	NPC479305

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC85131 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4635
0.1-0.2	4468
0.2-0.3	43
0.3-0.4	3
0.4-0.5	0
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
0.5738	Remote Similarity	NPD1510	Phase 2

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