NPASS Compound

Natural Product: NPC605361

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 29 31 0 0 0 0 0 0 0 0999 V2000 -2.0676 -2.0925 -1.7904 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4244 -1.2742 -1.0847 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0283 -1.1896 -1.1439 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7048 -0.3081 -0.3878 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1557 -0.2464 -0.4741 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8184 0.6780 0.3294 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1946 0.7960 0.3036 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9729 0.0077 -0.5151 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3248 -0.9098 -1.3136 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9346 -1.0250 -1.2838 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0231 0.4810 0.4220 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2808 0.4629 0.5348 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9155 1.3362 1.4191 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2873 1.3438 1.5627 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8672 2.2335 2.4571 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0252 0.4562 0.8013 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4188 -0.4174 -0.0806 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1283 -1.3195 -0.8584 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0441 -0.4099 -0.2102 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4784 -1.8507 -1.8161 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2330 1.3169 0.9885 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7280 1.5190 0.9305 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0652 0.1029 -0.5342 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9366 -1.5276 -1.9555 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4688 -1.7550 -1.9240 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3463 2.0304 2.0154 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8120 2.1712 2.7810 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0966 0.4559 0.9075 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2966 -1.0655 -1.8222 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 2 0 4 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 14 16 2 0 16 17 1 0 17 18 1 0 17 19 2 0 19 2 1 0 10 5 1 0 19 12 1 0 3 20 1 0 6 21 1 0 7 22 1 0 8 23 1 0 9 24 1 0 10 25 1 0 13 26 1 0 15 27 1 0 16 28 1 0 18 29 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 NPC605361 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	37630
0.1-0.2	9966
0.2-0.3	1389
0.3-0.4	609
0.4-0.5	178
0.5-0.6	51
0.6-0.7	25
0.7-0.8	1
0.8-0.85	1
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	NPC78540
0.8182	Intermediate Similarity	NPC50898
0.7447	Intermediate Similarity	NPC279121
0.7292	Intermediate Similarity	NPC213216
0.7234	Intermediate Similarity	NPC175013
0.72	Intermediate Similarity	NPC231772
0.6809	Remote Similarity	NPC197425
0.68	Remote Similarity	NPC610974
0.6735	Remote Similarity	NPC274121
0.6667	Remote Similarity	NPC239312
0.6667	Remote Similarity	NPC187432
0.6538	Remote Similarity	NPC62536
0.6538	Remote Similarity	NPC120464
0.6538	Remote Similarity	NPC483773
0.6538	Remote Similarity	NPC601901
0.6481	Remote Similarity	NPC52005
0.6481	Remote Similarity	NPC12200
0.6364	Remote Similarity	NPC183950
0.6327	Remote Similarity	NPC57601
0.6327	Remote Similarity	NPC259713
0.6275	Remote Similarity	NPC201395
0.6207	Remote Similarity	NPC138299
0.6207	Remote Similarity	NPC111112
0.6182	Remote Similarity	NPC606638
0.6154	Remote Similarity	NPC293183
0.614	Remote Similarity	NPC605634
0.6102	Remote Similarity	NPC112954
0.6038	Remote Similarity	NPC184536
0.6038	Remote Similarity	NPC482122
0.6038	Remote Similarity	NPC127447
0.6038	Remote Similarity	NPC605617
0.5902	Remote Similarity	NPC34089
0.5902	Remote Similarity	NPC183
0.5902	Remote Similarity	NPC196179
0.5902	Remote Similarity	NPC254351
0.5849	Remote Similarity	NPC131624
0.5833	Remote Similarity	NPC301217
0.5833	Remote Similarity	NPC291746
0.5818	Remote Similarity	NPC600900
0.5769	Remote Similarity	NPC603959
0.5741	Remote Similarity	NPC194281
0.5714	Remote Similarity	NPC259757
0.5577	Remote Similarity	NPC130230
0.5577	Remote Similarity	NPC222713
0.5574	Remote Similarity	NPC288840
0.5556	Remote Similarity	NPC603692
0.5556	Remote Similarity	NPC610480
0.5538	Remote Similarity	NPC150908
0.5538	Remote Similarity	NPC600972
0.5455	Remote Similarity	NPC290830
0.5455	Remote Similarity	NPC275722
0.5455	Remote Similarity	NPC71061
0.5455	Remote Similarity	NPC72425
0.5455	Remote Similarity	NPC303485
0.5455	Remote Similarity	NPC239128
0.5424	Remote Similarity	NPC67322
0.5385	Remote Similarity	NPC116775
0.5385	Remote Similarity	NPC134796
0.5373	Remote Similarity	NPC272064
0.5373	Remote Similarity	NPC186227
0.537	Remote Similarity	NPC256042
0.5357	Remote Similarity	NPC18260
0.5357	Remote Similarity	NPC602791
0.5345	Remote Similarity	NPC606140
0.5312	Remote Similarity	NPC224714
0.5294	Remote Similarity	NPC215203
0.5294	Remote Similarity	NPC143851
0.5283	Remote Similarity	NPC296197
0.5283	Remote Similarity	NPC169749
0.5283	Remote Similarity	NPC20791
0.5217	Remote Similarity	NPC601565
0.5192	Remote Similarity	NPC172262
0.5185	Remote Similarity	NPC179271
0.5179	Remote Similarity	NPC241498
0.5179	Remote Similarity	NPC306821
0.5179	Remote Similarity	NPC187498
0.5179	Remote Similarity	NPC609062
0.5161	Remote Similarity	NPC488612
0.5161	Remote Similarity	NPC602829
0.5088	Remote Similarity	NPC234133
0.5085	Remote Similarity	NPC608539
0.5079	Remote Similarity	NPC14871

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605361 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7093
0.1-0.2	1972
0.2-0.3	71
0.3-0.4	9
0.4-0.5	3
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7447	Intermediate Similarity	NPD1511	Phase 2
0.5283	Remote Similarity	NPD1512	Phase 3

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