NPASS Compound

Natural Product: NPC607416

Natural Product ID	NPC607416
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BJKGQODYLJQOBA-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1443601
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0001911] Anthracenecarboxylic acids and derivatives [CHEMONTID:0002424] Anthracenecarboxylic acids

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 31 33 0 0 0 0 0 0 0 0999 V2000 6.0362 0.2535 -0.3047 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6889 0.6190 -0.4754 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6161 -0.1549 -0.0724 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8846 -1.2525 0.4803 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2313 0.2562 -0.2658 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9200 1.4550 -0.8694 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5984 1.8162 -1.0383 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4230 0.9746 -0.6015 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1303 -0.2289 0.0046 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2104 -0.5646 0.1604 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4776 -1.7727 0.7691 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1784 -1.1468 0.4803 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8666 -2.2354 1.0280 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5527 -0.7559 0.2969 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5842 -1.5946 0.7324 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8911 -1.1945 0.5437 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2050 0.0009 -0.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1886 0.8266 -0.4868 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8682 0.4533 -0.3118 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8309 1.3623 -0.7829 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0851 2.4581 -1.3349 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1672 -0.7485 0.1446 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5021 0.2981 -1.3291 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6033 0.9833 0.3127 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7483 2.0671 -1.1879 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3585 2.7609 -1.5139 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3908 -2.6108 0.1833 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3256 -2.5277 1.2020 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6566 -1.8756 0.8966 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2465 0.3082 -0.2026 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4013 1.7704 -0.9623 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 3 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 12 13 2 0 12 14 1 0 14 15 2 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 10 5 1 0 19 14 1 0 20 8 1 0 1 22 1 0 1 23 1 0 1 24 1 0 6 25 1 0 7 26 1 0 11 27 1 0 15 28 1 0 16 29 1 0 17 30 1 0 18 31 1 0 M END

Standard InCHIKey	BJKGQODYLJQOBA-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C16H10O5/c1-21-16(20)11-7-6-10-12(15(11)19)14(18)9-5-3-2-4-8(9)13(10)17/h2-7,19H,1H3
SMILES	COC(=O)c1ccc2c(c1O)C(=O)c1ccccc1C2=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
NPO51421	Rubia wallichiana DECNE	Genus	Rubiaceae	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
Potency	39
AC50	7
EC50	2
IC50	4
CC50	3

Activity Type	# Activity
Individual protein	39
Cell line	1
Unchecked	14
Organism	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT10	Individual protein	Geminin	Homo sapiens	Potency	n.a.	18356.4	nM	PubChem BioAssay data set
NPT152	Individual protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	3662.6	nM	PubChem BioAssay data set
NPT1282	Individual protein	Microphthalmia-associated transcription factor	Homo sapiens	AC50	=	1612.0	nM	PubChem BioAssay data set
NPT1282	Individual protein	Microphthalmia-associated transcription factor	Homo sapiens	AC50	=	2824.0	nM	PubChem BioAssay data set
NPT1282	Individual protein	Microphthalmia-associated transcription factor	Homo sapiens	AC50	=	3740.0	nM	PubChem BioAssay data set
NPT152	Individual protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	3264.3	nM	PubChem BioAssay data set
NPT157	Individual protein	Breast cancer type 1 susceptibility protein	Homo sapiens	Potency	n.a.	31622.8	nM	PubChem BioAssay data set
NPT160	Individual protein	TAR DNA-binding protein 43	Homo sapiens	Potency	n.a.	7943.3	nM	PubChem BioAssay data set
NPT1415	Individual protein	Heat shock factor protein 1	Mus musculus	EC50	=	3732.0	nM	PubChem BioAssay data set
NPT105	Individual protein	Muscleblind-like protein 1	Homo sapiens	Potency	n.a.	1995.3	nM	PubChem BioAssay data set
NPT2867	Individual protein	Protein RecA	Mycobacterium tuberculosis	EC50	=	925.0	nM	PubChem BioAssay data set
NPT2866	Individual protein	Replicative DNA helicase	Mycobacterium tuberculosis	AC50	=	359300.0	nM	PubChem BioAssay data set
NPT2866	Individual protein	Replicative DNA helicase	Mycobacterium tuberculosis	AC50	=	51390.0	nM	PubChem BioAssay data set
NPT159	Individual protein	Aberrant vpr protein	Human immunodeficiency virus 1	Potency	n.a.	4466.8	nM	PubChem BioAssay data set
NPT101	Individual protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency	n.a.	2511.9	nM	PubChem BioAssay data set
NPT10	Individual protein	Geminin	Homo sapiens	Potency	n.a.	29092.9	nM	PubChem BioAssay data set
NPT55	Individual protein	Putative fructose-1,6-bisphosphate aldolase	Giardia intestinalis	Potency	=	500.0	nM	PubChem BioAssay data set
NPT531	Individual protein	Nuclear receptor ROR-gamma	Mus musculus	Potency	=	1122.0	nM	PubChem BioAssay data set
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	23109.3	nM	PubChem BioAssay data set
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	20596.2	nM	PubChem BioAssay data set
NPT484	Individual protein	Luciferin 4-monooxygenase	Photinus pyralis	Potency	n.a.	8492.1	nM	PubChem BioAssay data set
NPT54	Individual protein	Nonstructural protein 1	Influenza A virus	Potency	=	2238.7	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	5623.4	nM	PubChem BioAssay data set
NPT478	Individual protein	Ataxin-2	Homo sapiens	Potency	n.a.	35481.3	nM	PubChem BioAssay data set
NPT535	Individual protein	Parathyroid hormone receptor	Homo sapiens	Potency	n.a.	10000.0	nM	PubChem BioAssay data set
NPT583	Individual protein	Inositol monophosphatase 1	Rattus norvegicus	Potency	=	28183.8	nM	PubChem BioAssay data set
NPT63	Individual protein	Bromodomain adjacent to zinc finger domain protein 2B	Homo sapiens	Potency	n.a.	7943.3	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	12589.3	nM	PubChem BioAssay data set
NPT861	Individual protein	Isocitrate dehydrogenase [NADP] cytoplasmic	Homo sapiens	Potency	n.a.	29092.9	nM	PubChem BioAssay data set
NPT8	Individual protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	12589.3	nM	PubChem BioAssay data set
NPT755	Individual protein	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	Homo sapiens	Potency	n.a.	42561.5	nM	PubChem BioAssay data set
NPT64	Individual protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	6513.1	nM	PubChem BioAssay data set
NPT539	Individual protein	Cellular tumor antigen p53	Homo sapiens	Potency	n.a.	6309.6	nM	PubChem BioAssay data set
NPT53	Individual protein	4'-phosphopantetheinyl transferase ffp	Bacillus subtilis	Potency	=	22387.2	nM	PubChem BioAssay data set
NPT5	Individual protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency	n.a.	12589.3	nM	PubChem BioAssay data set
NPT64	Individual protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	32642.7	nM	PubChem BioAssay data set
NPT532	Individual protein	Lysine-specific demethylase 4A	Homo sapiens	Potency	n.a.	35481.3	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT71	Cell line	HEK293	Homo sapiens	Potency	n.a.	18348.9	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	IC50	=	65370.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	10691.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	25929.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	IC50	n.a.	1440.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	IC50	=	83620.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	IC50	n.a.	4520.0	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	4147.5	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	23099.9	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	3662.6	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	29092.9	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	22387.2	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	CC50	=	24175.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	CC50	>	40000.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	CC50	>	20000.0	nM	PubChem BioAssay data set

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 NPC607416 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	22110
0.1-0.2	24711
0.2-0.3	2788
0.3-0.4	198
0.4-0.5	38
0.5-0.6	11
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	Natural Product ID
0.6053	Remote Similarity	NPC142956
0.5946	Remote Similarity	NPC300274
0.575	Remote Similarity	NPC31799
0.5263	Remote Similarity	NPC128825
0.5227	Remote Similarity	NPC193703
0.5135	Remote Similarity	NPC96915
0.5135	Remote Similarity	NPC375356
0.5122	Remote Similarity	NPC53206
0.5122	Remote Similarity	NPC73061
0.5122	Remote Similarity	NPC294226
0.5116	Remote Similarity	NPC73416
0.5106	Remote Similarity	NPC604901

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607416 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3506
0.1-0.2	5325
0.2-0.3	302
0.3-0.4	14
0.4-0.5	1
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
0.5263	Remote Similarity	NPD9493	Phase 4

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