NPASS Compound

Natural Product: NPC483773

Natural Product ID	NPC483773
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	XFWVHODJBGMKRO-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10881558
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002595] 3'-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 -4.0739 -3.4071 0.6176 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4528 -2.0682 0.5706 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5282 -1.0323 0.4219 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1631 -1.3119 0.3131 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2706 -0.3015 0.1689 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7748 0.9921 0.1362 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0965 1.2924 0.2398 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0159 0.2566 0.3880 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5927 2.5719 0.2072 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8302 3.7368 0.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1732 -0.4991 0.0478 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7593 -1.7363 0.0695 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1477 -1.8672 -0.0506 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7278 -2.9797 -0.0360 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8895 -0.7139 -0.1897 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2709 -0.7348 -0.3159 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0243 0.4124 -0.4557 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3831 1.6333 -0.4713 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0106 1.6741 -0.3472 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2491 0.5089 -0.2055 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9593 0.5334 -0.0880 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0871 2.8396 -0.6102 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9049 -1.9628 -0.2992 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9308 -3.9978 1.0428 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2016 -3.5120 1.2860 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9005 -3.8595 -0.3936 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8217 -2.3393 0.3445 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0571 1.8157 0.0197 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0861 0.4689 0.4737 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9758 3.5186 -0.6209 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3995 4.5726 -0.3960 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4205 4.0154 1.0561 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1728 -2.6252 0.1780 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1001 0.4034 -0.5545 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4866 2.6178 -0.3566 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4402 3.1414 -1.5218 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8057 -2.0566 -0.7336 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 7 9 1 0 9 10 1 0 5 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 18 22 1 0 16 23 1 0 8 3 1 0 21 11 1 0 20 15 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 6 28 1 0 8 29 1 0 10 30 1 0 10 31 1 0 10 32 1 0 12 33 1 0 17 34 1 0 19 35 1 0 22 36 1 0 23 37 1 0 M END

Standard InCHIKey	XFWVHODJBGMKRO-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C17H14O6/c1-21-11-3-9(4-12(7-11)22-2)15-8-14(20)17-13(19)5-10(18)6-16(17)23-15/h3-8,18-19H,1-2H3
SMILES	COc1cc(cc(c1)OC)c1cc(=O)c2c(cc(cc2o1)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
NPO40877	Malagasy connaraceous	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[14510616]

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
Cell line	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
NPT521	Cell line	RBL-2H3	Rattus norvegicus	IC50	>	500000.0	nM	PMID[14510616]

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 NPC483773 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	29819
0.1-0.2	16683
0.2-0.3	2212
0.3-0.4	832
0.4-0.5	211
0.5-0.6	80
0.6-0.7	10
0.7-0.8	0
0.8-0.85	2
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	NPC62536
0.8039	Intermediate Similarity	NPC120464
0.7692	Intermediate Similarity	NPC231772
0.7358	Intermediate Similarity	NPC601901
0.7273	Intermediate Similarity	NPC12200
0.7273	Intermediate Similarity	NPC606638
0.7143	Intermediate Similarity	NPC183950
0.6964	Remote Similarity	NPC52005
0.6909	Remote Similarity	NPC600900
0.6538	Remote Similarity	NPC50898
0.6538	Remote Similarity	NPC78540
0.6415	Remote Similarity	NPC175013
0.6349	Remote Similarity	NPC183
0.6333	Remote Similarity	NPC605634
0.6296	Remote Similarity	NPC279121
0.6029	Remote Similarity	NPC63454
0.6029	Remote Similarity	NPC183851
0.597	Remote Similarity	NPC150908
0.5882	Remote Similarity	NPC303485
0.5862	Remote Similarity	NPC33265
0.5862	Remote Similarity	NPC48479
0.5797	Remote Similarity	NPC186227
0.5735	Remote Similarity	NPC600972
0.5714	Remote Similarity	NPC274121
0.569	Remote Similarity	NPC284552
0.569	Remote Similarity	NPC219330
0.569	Remote Similarity	NPC605617
0.5652	Remote Similarity	NPC290830
0.5652	Remote Similarity	NPC71061
0.5652	Remote Similarity	NPC72425
0.5634	Remote Similarity	NPC601565
0.5614	Remote Similarity	NPC213216
0.5593	Remote Similarity	NPC59951
0.5593	Remote Similarity	NPC241838
0.5593	Remote Similarity	NPC234133
0.5593	Remote Similarity	NPC28274
0.5593	Remote Similarity	NPC610359
0.5574	Remote Similarity	NPC162351
0.5574	Remote Similarity	NPC609179
0.5571	Remote Similarity	NPC272064
0.5541	Remote Similarity	NPC101731
0.5538	Remote Similarity	NPC112954
0.5517	Remote Similarity	NPC610974
0.5493	Remote Similarity	NPC215203
0.5484	Remote Similarity	NPC133953
0.5467	Remote Similarity	NPC172202
0.5467	Remote Similarity	NPC284127
0.5439	Remote Similarity	NPC483772
0.5424	Remote Similarity	NPC241498
0.5424	Remote Similarity	NPC123886
0.5424	Remote Similarity	NPC184536
0.5424	Remote Similarity	NPC127447
0.5424	Remote Similarity	NPC156222
0.5424	Remote Similarity	NPC103342
0.5424	Remote Similarity	NPC29353
0.541	Remote Similarity	NPC159103
0.5362	Remote Similarity	NPC134796
0.5333	Remote Similarity	NPC286342
0.5333	Remote Similarity	NPC50403
0.5333	Remote Similarity	NPC184136
0.5323	Remote Similarity	NPC177298
0.5323	Remote Similarity	NPC195202
0.5323	Remote Similarity	NPC603596
0.5303	Remote Similarity	NPC301217
0.5278	Remote Similarity	NPC143851
0.5263	Remote Similarity	NPC88023
0.5263	Remote Similarity	NPC165970
0.5263	Remote Similarity	NPC309025
0.5256	Remote Similarity	NPC84324
0.5254	Remote Similarity	NPC293183
0.5254	Remote Similarity	NPC75279
0.5246	Remote Similarity	NPC108406
0.5246	Remote Similarity	NPC603662
0.5238	Remote Similarity	NPC125062
0.5238	Remote Similarity	NPC279989
0.5238	Remote Similarity	NPC137062
0.5195	Remote Similarity	NPC288131
0.5167	Remote Similarity	NPC301323
0.5167	Remote Similarity	NPC600177
0.5161	Remote Similarity	NPC82325
0.5161	Remote Similarity	NPC54394
0.5161	Remote Similarity	NPC83508
0.5161	Remote Similarity	NPC328119
0.5161	Remote Similarity	NPC255350
0.5156	Remote Similarity	NPC483775
0.5152	Remote Similarity	NPC138299
0.5152	Remote Similarity	NPC111112
0.5147	Remote Similarity	NPC34089
0.5147	Remote Similarity	NPC196179
0.5082	Remote Similarity	NPC100887
0.5082	Remote Similarity	NPC266597
0.5082	Remote Similarity	NPC276409
0.5079	Remote Similarity	NPC124784
0.5079	Remote Similarity	NPC223579
0.5075	Remote Similarity	NPC291746
0.5072	Remote Similarity	NPC224714
0.5062	Remote Similarity	NPC476410

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC483773 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5488
0.1-0.2	3588
0.2-0.3	64
0.3-0.4	7
0.4-0.5	1
0.5-0.6	1
0.6-0.7	1
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
0.6296	Remote Similarity	NPD1511	Phase 2
0.5161	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