NPASS Compound

Natural Product: NPC607923

Natural Product ID	NPC607923
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	QLPJSBWLIFSIMS-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3311041
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 43 46 0 0 0 0 0 0 0 0999 V2000 8.0494 0.4200 0.4527 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2320 -0.6671 0.7709 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8513 -0.5643 0.6630 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2550 0.5993 0.2439 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8622 0.6518 0.1521 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0806 -0.4353 0.4722 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6365 -0.3164 0.3557 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0800 0.2723 -0.7612 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2266 0.3912 -0.8887 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0829 -0.0182 -0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4273 0.1492 -0.2305 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3278 -0.2943 0.7188 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8472 -0.9003 1.8761 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4920 -1.0593 2.0790 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5910 -0.6187 1.1351 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7658 -0.7721 1.3268 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2378 -1.3078 2.3457 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6753 -0.1216 0.4885 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2432 0.4719 -0.6367 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0395 1.6901 -0.1891 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2171 -0.4699 -1.3370 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2641 0.9364 -1.6340 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9713 0.7765 -1.4245 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6953 -1.5960 0.8914 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0891 -1.6734 0.9915 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9218 1.1861 1.2499 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1063 0.1062 0.3305 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7412 0.8815 -0.4944 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8430 1.4627 -0.0121 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3724 1.5558 -0.1749 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6700 0.6613 -1.5775 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5816 -1.2328 2.5928 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1329 -1.5337 2.9861 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5313 2.1606 -1.0643 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8277 1.4125 0.5253 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3297 2.4575 0.2208 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3595 -1.4072 -0.7445 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8778 -0.7285 -2.3499 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2269 -0.0173 -1.4265 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6261 1.4185 -2.5561 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2647 1.1323 -2.1848 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1269 -2.4640 1.1499 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5468 -2.5954 1.3228 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 9 10 1 0 10 11 2 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 12 18 1 0 18 19 1 0 19 20 1 0 19 21 1 0 19 22 1 0 22 23 2 0 6 24 1 0 24 25 2 0 25 3 1 0 16 7 1 0 15 10 1 0 23 11 1 0 1 26 1 0 1 27 1 0 1 28 1 0 4 29 1 0 5 30 1 0 8 31 1 0 13 32 1 0 14 33 1 0 20 34 1 0 20 35 1 0 20 36 1 0 21 37 1 0 21 38 1 0 21 39 1 0 22 40 1 0 23 41 1 0 24 42 1 0 25 43 1 0 M END

Standard InCHIKey	QLPJSBWLIFSIMS-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C21H18O4/c1-21(2)11-10-15-18(25-21)9-8-16-19(22)17(12-24-20(15)16)13-4-6-14(23-3)7-5-13/h4-12H,1-3H3
SMILES	COc1ccc(-c2coc3c4c(ccc3c2=O)OC(C)(C)C=C4)cc1

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
NPO57474	Millettia dura	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
IC50	6

Activity Type	# Activity
Cell line	5
Non-molecular	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
NPT65	Cell line	HepG2	Homo sapiens	IC50	>	10000.0	nM	PMID[24863745]
NPT737	Cell line	HUVEC	Homo sapiens	IC50	>	10000.0	nM	PMID[24863745]
NPT380	Cell line	U-251	Homo sapiens	IC50	>	10000.0	nM	PMID[24863745]
NPT319	Cell line	B16	Mus musculus	IC50	>	10000.0	nM	PMID[24863745]
NPT1083	Cell line	A-375	Homo sapiens	IC50	>	10000.0	nM	PMID[24863745]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[24863745]

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 NPC607923 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	25678
0.1-0.2	21771
0.2-0.3	1960
0.3-0.4	330
0.4-0.5	85
0.5-0.6	23
0.6-0.7	4
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
0.8065	Intermediate Similarity	NPC608710
0.7833	Intermediate Similarity	NPC600644
0.7619	Intermediate Similarity	NPC113055
0.746	Intermediate Similarity	NPC128961
0.6935	Remote Similarity	NPC478987
0.6765	Remote Similarity	NPC273021
0.6716	Remote Similarity	NPC51759
0.6615	Remote Similarity	NPC488135
0.5946	Remote Similarity	NPC604503
0.5652	Remote Similarity	NPC24673
0.5574	Remote Similarity	NPC182428
0.5469	Remote Similarity	NPC474340
0.5395	Remote Similarity	NPC229847
0.5385	Remote Similarity	NPC136095
0.5362	Remote Similarity	NPC602756
0.5312	Remote Similarity	NPC474264
0.5294	Remote Similarity	NPC157855
0.5256	Remote Similarity	NPC5840
0.5231	Remote Similarity	NPC333691
0.5217	Remote Similarity	NPC254741
0.52	Remote Similarity	NPC104406
0.5143	Remote Similarity	NPC13967
0.5135	Remote Similarity	NPC482699
0.5135	Remote Similarity	NPC179970
0.5132	Remote Similarity	NPC184755
0.5132	Remote Similarity	NPC18284
0.5079	Remote Similarity	NPC120924
0.5067	Remote Similarity	NPC261470
0.5067	Remote Similarity	NPC302741
0.5067	Remote Similarity	NPC144162
0.5065	Remote Similarity	NPC180340

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607923 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3931
0.1-0.2	5095
0.2-0.3	119
0.3-0.4	4
0.4-0.5	1
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