NPASS Compound

Natural Product: NPC602789

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 58 63 0 0 0 0 0 0 0 0999 V2000 -8.1054 1.1575 2.0095 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2281 0.8427 1.1821 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9185 1.2192 1.3924 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9623 0.8656 0.4727 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5508 1.2325 0.6327 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1036 1.9540 1.7170 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7436 2.2612 1.7923 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8375 1.8750 0.8342 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4884 2.1969 0.9494 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4995 1.4100 1.4538 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5831 1.0826 0.6223 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6161 0.3128 1.0466 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7328 -0.0139 0.1616 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8372 0.4135 -1.1390 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9150 0.0845 -1.9570 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0094 0.4720 -3.1356 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9023 -0.6971 -1.4293 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0041 -1.0584 -2.1993 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0970 -0.6136 -3.5277 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9972 -1.8481 -1.6594 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8815 -2.2705 -0.3546 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8961 -3.0756 0.1923 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7846 -1.9032 0.3914 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7561 -1.1032 -0.1202 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7291 -0.7743 0.6184 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5734 -0.1526 2.3512 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5365 0.1370 3.2099 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4943 0.9297 2.7390 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4753 1.1932 3.6383 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3022 1.1408 -0.2664 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6347 0.8359 -0.3471 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2813 0.1774 -0.5972 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5056 -0.1929 -0.8249 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7576 -0.9193 -1.9820 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0296 -1.3325 -2.2675 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2857 -2.0586 -3.4227 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0471 -1.0107 -1.3818 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7969 -0.2951 -0.2425 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8235 0.0116 0.6205 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5201 0.1153 0.0365 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6553 1.7906 2.2811 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7648 2.2917 2.5122 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4263 2.8469 2.6694 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5422 1.4826 -0.3772 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0698 1.0265 -1.5634 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9163 -0.1167 -3.8463 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8741 -2.1492 -2.2360 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7352 -4.0865 0.1698 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6885 -2.2295 1.4099 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3898 -0.7678 2.7046 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5114 -0.2334 4.2341 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5965 1.8327 4.4201 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5684 0.8470 -1.0105 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9877 0.2692 -1.1985 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9175 -1.1461 -2.6469 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2363 -2.2048 -3.7584 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0457 -1.3449 -1.6225 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0970 -0.7094 1.2848 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 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 1 0 13 14 2 0 14 15 1 0 15 16 2 0 15 17 1 0 17 18 2 0 18 19 1 0 18 20 1 0 20 21 2 0 21 22 1 0 21 23 1 0 23 24 2 0 24 25 1 0 12 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 8 30 1 0 30 31 2 0 4 32 1 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 35 37 2 0 37 38 1 0 38 39 1 0 38 40 2 0 40 2 1 0 31 5 1 0 40 33 1 0 28 10 1 0 25 13 1 0 24 17 1 0 3 41 1 0 6 42 1 0 7 43 1 0 11 44 1 0 14 45 1 0 19 46 1 0 20 47 1 0 22 48 1 0 23 49 1 0 26 50 1 0 27 51 1 0 29 52 1 0 30 53 1 0 31 54 1 0 34 55 1 0 36 56 1 0 37 57 1 0 39 58 1 0 M END

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

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

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

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 NPC602789 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	35662
0.1-0.2	11986
0.2-0.3	1377
0.3-0.4	654
0.4-0.5	136
0.5-0.6	26
0.6-0.7	11
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC112954
0.7231	Intermediate Similarity	NPC34089
0.7231	Intermediate Similarity	NPC196179
0.697	Remote Similarity	NPC183
0.6667	Remote Similarity	NPC50898
0.6667	Remote Similarity	NPC183950
0.642	Remote Similarity	NPC219927
0.642	Remote Similarity	NPC611172
0.6389	Remote Similarity	NPC272064
0.629	Remote Similarity	NPC231772
0.625	Remote Similarity	NPC12200
0.6167	Remote Similarity	NPC279121
0.6102	Remote Similarity	NPC78540
0.6	Remote Similarity	NPC52005
0.597	Remote Similarity	NPC605634
0.56	Remote Similarity	NPC303485
0.5571	Remote Similarity	NPC138299
0.5571	Remote Similarity	NPC111112
0.5556	Remote Similarity	NPC213216
0.5538	Remote Similarity	NPC62536
0.5538	Remote Similarity	NPC120464
0.5538	Remote Similarity	NPC483773
0.5538	Remote Similarity	NPC601901
0.5522	Remote Similarity	NPC606638
0.5484	Remote Similarity	NPC175013
0.5397	Remote Similarity	NPC274121
0.5395	Remote Similarity	NPC71061
0.5395	Remote Similarity	NPC72425
0.5385	Remote Similarity	NPC601565
0.5278	Remote Similarity	NPC291746
0.5263	Remote Similarity	NPC600972
0.5256	Remote Similarity	NPC215203
0.5231	Remote Similarity	NPC610974
0.52	Remote Similarity	NPC259757
0.5195	Remote Similarity	NPC290830
0.5135	Remote Similarity	NPC254351
0.5122	Remote Similarity	NPC601710
0.5119	Remote Similarity	NPC4390
0.5068	Remote Similarity	NPC301217
0.5065	Remote Similarity	NPC150908

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602789 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7284
0.1-0.2	1823
0.2-0.3	37
0.3-0.4	3
0.4-0.5	2
0.5-0.6	0
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
0.6167	Remote Similarity	NPD1511	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