NPASS Compound

Natural Product: NPC246948

Natural Product ID	NPC246948
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Cajaflavanone
IUPAC Name	(2S)-5-hydroxy-2-(4-hydroxyphenyl)-8,8-dimethyl-6-(3-methylbut-2-enyl)-2,3-dihydropyrano[2,3-h]chromen-4-one
Synonyms	Cajaflavanone
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL557692
PubChem CID	15224381
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003646] 6-prenylated flavans [CHEMONTID:0003507] 6-prenylated flavanones

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 56 59 0 0 0 0 0 0 0 0999 V2000 -5.7490 1.9890 -1.8433 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9832 1.7490 -0.5951 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1928 0.7025 -0.5121 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3970 0.3844 0.6796 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9327 0.2992 0.4278 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1236 1.3991 0.2569 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2460 1.3026 0.0219 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0917 2.4741 -0.1557 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5761 3.5838 -0.4198 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5648 2.3776 -0.0287 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0078 1.0842 -0.6602 C 0 0 1 0 0 0 0 0 0 0 0 0 4.4055 0.8200 -0.2007 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9357 -0.4332 -0.4053 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2367 -0.7268 0.0089 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0010 0.2364 0.6263 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4744 1.4836 0.8302 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1884 1.7692 0.4193 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2951 -0.0622 1.0361 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1916 0.0222 -0.2801 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 0.0686 -0.0474 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0491 -1.0420 0.1212 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6444 -2.3645 0.0572 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1150 -3.4246 0.2210 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5760 -3.3712 0.4740 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8218 -4.0300 1.8387 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2384 -4.2543 -0.5563 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1000 -2.0781 0.5228 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3058 -0.9448 0.3536 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6744 2.6590 0.3176 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1599 2.7182 0.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4362 2.8518 -1.7605 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3135 1.0917 -2.1719 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0098 2.2632 -2.6445 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1206 0.0363 -1.3644 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7352 -0.6296 1.0478 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6306 1.0658 1.5203 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8396 2.3152 1.0598 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0684 3.2500 -0.4793 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0102 1.2637 -1.7736 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3230 -1.1710 -0.8891 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6006 -1.7301 -0.1786 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0754 2.2370 1.3144 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7870 2.7435 0.5828 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9594 0.6848 1.2180 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7001 -2.4894 -0.1226 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3132 -4.4309 0.1764 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3364 -5.0255 1.8460 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8879 -4.0860 2.0656 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2957 -3.4153 2.6201 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2085 -3.8139 -0.9262 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5809 -4.4437 -1.4374 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5138 -5.2469 -0.1335 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3028 3.3539 0.9499 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2967 3.3959 0.5329 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2912 2.2233 1.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0982 3.3152 0.3798 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 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 15 18 1 0 11 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 1 0 24 26 1 0 24 27 1 0 27 28 1 0 6 29 1 0 2 30 1 0 28 5 1 0 20 7 2 0 28 21 2 0 17 12 1 0 1 31 1 0 1 32 1 0 1 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 10 37 1 0 10 38 1 0 11 39 1 6 13 40 1 0 14 41 1 0 16 42 1 0 17 43 1 0 18 44 1 0 22 45 1 0 23 46 1 0 25 47 1 0 25 48 1 0 25 49 1 0 26 50 1 0 26 51 1 0 26 52 1 0 29 53 1 0 30 54 1 0 30 55 1 0 30 56 1 0 M END

Standard InCHIKey	TXWYWZHIUMRYOS-FQEVSTJZSA-N
Standard InCHI	InChI=1S/C25H26O5/c1-14(2)5-10-17-22(28)21-19(27)13-20(15-6-8-16(26)9-7-15)29-24(21)18-11-12-25(3,4)30-23(17)18/h5-9,11-12,20,26,28H,10,13H2,1-4H3/t20-/m0/s1
SMILES	CC(=CCc1c(c2C(=O)C[C@@H](c3ccc(cc3)O)Oc2c2C=CC(C)(C)Oc12)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
NPO13293	Lespedeza floribunda	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[19132934]
NPO13293	Lespedeza floribunda	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[19132934]
NPO13293	Lespedeza floribunda	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13293	Lespedeza floribunda	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	1

Activity Type	# Activity
Others	1

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
NPT2	Others	Unspecified	n.a.	IC50	=	8410.0	nM	PMID[22037378]

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 NPC246948 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	19413
0.1-0.2	25991
0.2-0.3	3591
0.3-0.4	628
0.4-0.5	162
0.5-0.6	52
0.6-0.7	9
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
0.8308	Intermediate Similarity	NPC214774
0.7941	Intermediate Similarity	NPC119209
0.7794	Intermediate Similarity	NPC192686
0.7794	Intermediate Similarity	NPC284820
0.7576	Intermediate Similarity	NPC142405
0.7031	Intermediate Similarity	NPC265040
0.6818	Remote Similarity	NPC311741
0.6522	Remote Similarity	NPC473078
0.6438	Remote Similarity	NPC195621
0.6364	Remote Similarity	NPC107572
0.6364	Remote Similarity	NPC32739
0.6269	Remote Similarity	NPC69674
0.6269	Remote Similarity	NPC75049
0.6081	Remote Similarity	NPC67805
0.6027	Remote Similarity	NPC180301
0.597	Remote Similarity	NPC164980
0.5942	Remote Similarity	NPC610133
0.589	Remote Similarity	NPC39752
0.5844	Remote Similarity	NPC132592
0.5775	Remote Similarity	NPC608140
0.5769	Remote Similarity	NPC483810
0.5733	Remote Similarity	NPC475052
0.5714	Remote Similarity	NPC54577
0.5714	Remote Similarity	NPC176229
0.5714	Remote Similarity	NPC220998
0.5714	Remote Similarity	NPC160821
0.5714	Remote Similarity	NPC83357
0.5634	Remote Similarity	NPC285555
0.5634	Remote Similarity	NPC76338
0.5634	Remote Similarity	NPC250242
0.5571	Remote Similarity	NPC187282
0.557	Remote Similarity	NPC283234
0.5513	Remote Similarity	NPC101793
0.5513	Remote Similarity	NPC110303
0.5513	Remote Similarity	NPC601247
0.5513	Remote Similarity	NPC609256
0.5467	Remote Similarity	NPC166934
0.5467	Remote Similarity	NPC483807
0.5455	Remote Similarity	NPC40033
0.5455	Remote Similarity	NPC483808
0.5352	Remote Similarity	NPC250214
0.5333	Remote Similarity	NPC301276
0.5316	Remote Similarity	NPC111786
0.5294	Remote Similarity	NPC52576
0.5286	Remote Similarity	NPC76372
0.5286	Remote Similarity	NPC37496
0.5278	Remote Similarity	NPC66515
0.5278	Remote Similarity	NPC197252
0.525	Remote Similarity	NPC312273
0.5211	Remote Similarity	NPC324436
0.5211	Remote Similarity	NPC78
0.5211	Remote Similarity	NPC149796
0.5205	Remote Similarity	NPC234629
0.5195	Remote Similarity	NPC48579
0.5152	Remote Similarity	NPC167624
0.5152	Remote Similarity	NPC166482
0.5139	Remote Similarity	NPC148757
0.5132	Remote Similarity	NPC36275
0.5128	Remote Similarity	NPC161191
0.507	Remote Similarity	NPC169591
0.507	Remote Similarity	NPC298223
0.507	Remote Similarity	NPC604412
0.5068	Remote Similarity	NPC310130
0.5067	Remote Similarity	NPC470647
0.5063	Remote Similarity	NPC488428
0.5063	Remote Similarity	NPC488427
0.5062	Remote Similarity	NPC483809

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC246948 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3195
0.1-0.2	5836
0.2-0.3	112
0.3-0.4	4
0.4-0.5	3
0.5-0.6	0
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
		NPD

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