NPASS Compound

Natural Product: NPC605038

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 33 35 0 0 0 0 0 0 0 0999 V2000 5.3764 -0.1014 1.5156 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7331 0.2119 0.3162 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3547 0.3103 0.2099 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7106 1.5127 0.4233 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4753 2.6428 0.7519 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3634 1.6593 0.3308 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5981 0.5437 0.0055 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7006 0.6702 -0.0870 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5035 -0.3479 -0.3937 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9302 -0.1120 -0.4733 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8219 -1.1258 -0.7874 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1976 -0.8805 -0.8600 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6438 0.3994 -0.6103 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7733 1.4253 -0.2955 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4199 1.1658 -0.2281 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9429 -1.5792 -0.6216 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4433 -1.7660 -0.5346 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9715 -2.8852 -0.7399 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2137 -0.6697 -0.2132 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6035 -0.7835 -0.1092 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2076 -2.0279 -0.3360 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4686 -1.1803 1.7090 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8295 0.3892 2.3450 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3994 0.3483 1.5158 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2516 3.1375 1.6160 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8388 2.6068 0.4974 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5058 -2.1358 -0.9878 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8686 -1.6939 -1.1079 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7104 0.5872 -0.6672 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1227 2.4444 -0.0961 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6980 1.9270 0.0126 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5537 -2.4280 -0.8718 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5538 -2.2647 -1.2579 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 4 6 1 0 6 7 2 0 7 8 1 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 9 16 2 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 2 0 20 21 1 0 20 3 1 0 19 7 1 0 15 10 1 0 1 22 1 0 1 23 1 0 1 24 1 0 5 25 1 0 6 26 1 0 11 27 1 0 12 28 1 0 13 29 1 0 14 30 1 0 15 31 1 0 16 32 1 0 21 33 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 NPC605038 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	28666
0.1-0.2	17832
0.2-0.3	2448
0.3-0.4	602
0.4-0.5	213
0.5-0.6	65
0.6-0.7	13
0.7-0.8	1
0.8-0.85	2
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	NPC293183
0.8163	Intermediate Similarity	NPC241498
0.8163	Intermediate Similarity	NPC156222
0.7647	Intermediate Similarity	NPC100887
0.75	Intermediate Similarity	NPC256283
0.7451	Intermediate Similarity	NPC284552
0.7358	Intermediate Similarity	NPC83508
0.7358	Intermediate Similarity	NPC255350
0.7115	Intermediate Similarity	NPC239128
0.7115	Intermediate Similarity	NPC609062
0.6923	Remote Similarity	NPC26227
0.6667	Remote Similarity	NPC470402
0.6604	Remote Similarity	NPC602963
0.6481	Remote Similarity	NPC275722
0.6481	Remote Similarity	NPC127447
0.6364	Remote Similarity	NPC18260
0.6296	Remote Similarity	NPC131624
0.629	Remote Similarity	NPC213622
0.6182	Remote Similarity	NPC194281
0.6154	Remote Similarity	NPC239312
0.6154	Remote Similarity	NPC78540
0.6111	Remote Similarity	NPC201395
0.6034	Remote Similarity	NPC608539
0.5893	Remote Similarity	NPC306821
0.5893	Remote Similarity	NPC482122
0.5893	Remote Similarity	NPC187498
0.5789	Remote Similarity	NPC53181
0.5789	Remote Similarity	NPC184136
0.5789	Remote Similarity	NPC231772
0.5789	Remote Similarity	NPC145379
0.5789	Remote Similarity	NPC120163
0.5789	Remote Similarity	NPC601901
0.566	Remote Similarity	NPC197425
0.5636	Remote Similarity	NPC106461
0.5614	Remote Similarity	NPC203891
0.5614	Remote Similarity	NPC44079
0.5614	Remote Similarity	NPC266960
0.5614	Remote Similarity	NPC98661
0.5556	Remote Similarity	NPC41721
0.5517	Remote Similarity	NPC62536
0.5517	Remote Similarity	NPC163524
0.55	Remote Similarity	NPC160951
0.55	Remote Similarity	NPC52005
0.5455	Remote Similarity	NPC607644
0.5439	Remote Similarity	NPC472438
0.5439	Remote Similarity	NPC75279
0.5424	Remote Similarity	NPC9609
0.5424	Remote Similarity	NPC25270
0.5417	Remote Similarity	NPC475942
0.541	Remote Similarity	NPC183950
0.541	Remote Similarity	NPC47781
0.5357	Remote Similarity	NPC284424
0.5357	Remote Similarity	NPC278556
0.5345	Remote Similarity	NPC274327
0.5345	Remote Similarity	NPC488084
0.5345	Remote Similarity	NPC275836
0.5345	Remote Similarity	NPC29353
0.5333	Remote Similarity	NPC115798
0.5333	Remote Similarity	NPC69394
0.5333	Remote Similarity	NPC29841
0.5283	Remote Similarity	NPC143903
0.5273	Remote Similarity	NPC57601
0.5254	Remote Similarity	NPC198826
0.5254	Remote Similarity	NPC57030
0.5254	Remote Similarity	NPC234133
0.5254	Remote Similarity	NPC120464
0.5254	Remote Similarity	NPC483773
0.5254	Remote Similarity	NPC276409
0.5246	Remote Similarity	NPC12200
0.5246	Remote Similarity	NPC606638
0.5231	Remote Similarity	NPC14871
0.5185	Remote Similarity	NPC55557
0.5172	Remote Similarity	NPC601286
0.5172	Remote Similarity	NPC607196
0.5167	Remote Similarity	NPC148423
0.5167	Remote Similarity	NPC78913
0.5167	Remote Similarity	NPC217186
0.5167	Remote Similarity	NPC312924
0.5167	Remote Similarity	NPC603662
0.5167	Remote Similarity	NPC604312
0.5085	Remote Similarity	NPC301323
0.5085	Remote Similarity	NPC184536
0.5085	Remote Similarity	NPC47815
0.5085	Remote Similarity	NPC600177
0.5082	Remote Similarity	NPC292460
0.5082	Remote Similarity	NPC146165
0.5082	Remote Similarity	NPC212678
0.5077	Remote Similarity	NPC602829

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605038 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4683
0.1-0.2	4327
0.2-0.3	130
0.3-0.4	7
0.4-0.5	2
0.5-0.6	0
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
0.7358	Intermediate 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