NPASS Compound

Natural Product: NPC604328

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 5.6844 1.3996 -0.7716 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3271 1.6958 -0.9441 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3828 0.7951 -0.4185 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7786 -0.3500 0.2493 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8442 -1.2262 0.7606 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1941 -2.3866 1.4374 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4849 -0.9384 0.5930 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5253 -1.7934 1.0919 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8443 -2.8477 1.7068 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8157 -1.4499 0.8918 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1872 -0.3046 0.2238 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5936 0.0246 0.0321 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8954 1.1994 -0.6533 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2163 1.5946 -0.8836 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2598 0.8043 -0.4223 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5894 1.1396 -0.6177 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9718 -0.3562 0.2546 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6464 -0.7220 0.4677 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2226 0.4591 -0.2219 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0497 0.1904 -0.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0349 1.0476 -0.5656 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8528 0.3669 -1.1426 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8952 1.3553 0.3274 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3407 2.0930 -1.3096 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8183 -0.5431 0.3618 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2844 -3.2462 0.8965 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5324 -2.1477 1.2989 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1140 1.8353 -1.0244 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4551 2.4969 -1.4098 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3264 0.4759 -0.6977 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7934 -0.9561 0.6047 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4567 -1.6361 1.0010 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7347 1.9307 -1.0806 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 1 0 5 7 2 0 7 8 1 0 8 9 2 0 8 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 15 17 1 0 17 18 2 0 11 19 1 0 19 20 1 0 20 21 2 0 21 3 1 0 20 7 1 0 18 12 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 6 26 1 0 10 27 1 0 13 28 1 0 14 29 1 0 16 30 1 0 17 31 1 0 18 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 NPC604328 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	30139
0.1-0.2	15879
0.2-0.3	2639
0.3-0.4	705
0.4-0.5	312
0.5-0.6	127
0.6-0.7	27
0.7-0.8	0
0.8-0.85	3
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	NPC234133
0.8235	Intermediate Similarity	NPC108406
0.82	Intermediate Similarity	NPC127447
0.82	Intermediate Similarity	NPC29353
0.7778	Intermediate Similarity	NPC137062
0.7593	Intermediate Similarity	NPC124784
0.7541	Intermediate Similarity	NPC603508
0.7419	Intermediate Similarity	NPC600396
0.7358	Intermediate Similarity	NPC33265
0.7358	Intermediate Similarity	NPC48479
0.7302	Intermediate Similarity	NPC159707
0.7302	Intermediate Similarity	NPC194593
0.7273	Intermediate Similarity	NPC195202
0.7273	Intermediate Similarity	NPC223579
0.7077	Intermediate Similarity	NPC205026
0.7037	Intermediate Similarity	NPC198826
0.7037	Intermediate Similarity	NPC143799
0.7037	Intermediate Similarity	NPC146679
0.7037	Intermediate Similarity	NPC120163
0.697	Remote Similarity	NPC265624
0.6964	Remote Similarity	NPC177298
0.6909	Remote Similarity	NPC78913
0.6765	Remote Similarity	NPC55443
0.6727	Remote Similarity	NPC250266
0.6615	Remote Similarity	NPC158027
0.6552	Remote Similarity	NPC610914
0.6545	Remote Similarity	NPC241498
0.6515	Remote Similarity	NPC331652
0.6491	Remote Similarity	NPC328119
0.6462	Remote Similarity	NPC601984
0.6418	Remote Similarity	NPC39360
0.6418	Remote Similarity	NPC121649
0.6418	Remote Similarity	NPC29763
0.6418	Remote Similarity	NPC210003
0.6377	Remote Similarity	NPC27942
0.6308	Remote Similarity	NPC248739
0.625	Remote Similarity	NPC301323
0.625	Remote Similarity	NPC47815
0.6226	Remote Similarity	NPC50898
0.614	Remote Similarity	NPC231772
0.614	Remote Similarity	NPC87125
0.614	Remote Similarity	NPC188871
0.6129	Remote Similarity	NPC602829
0.6071	Remote Similarity	NPC607196
0.6056	Remote Similarity	NPC282169
0.6029	Remote Similarity	NPC14606
0.597	Remote Similarity	NPC600972
0.5965	Remote Similarity	NPC71334
0.5965	Remote Similarity	NPC275836
0.5882	Remote Similarity	NPC290830
0.5862	Remote Similarity	NPC57030
0.5862	Remote Similarity	NPC145379
0.5862	Remote Similarity	NPC231018
0.5857	Remote Similarity	NPC18699
0.5797	Remote Similarity	NPC272064
0.5781	Remote Similarity	NPC265932
0.5763	Remote Similarity	NPC159275
0.5763	Remote Similarity	NPC25270
0.5763	Remote Similarity	NPC162313
0.5763	Remote Similarity	NPC603662
0.5738	Remote Similarity	NPC183950
0.5738	Remote Similarity	NPC252933
0.5738	Remote Similarity	NPC78326
0.5714	Remote Similarity	NPC44931
0.5714	Remote Similarity	NPC215203
0.569	Remote Similarity	NPC275722
0.569	Remote Similarity	NPC52611
0.569	Remote Similarity	NPC103904
0.569	Remote Similarity	NPC262094
0.569	Remote Similarity	NPC152042
0.569	Remote Similarity	NPC239128
0.5634	Remote Similarity	NPC95090
0.5634	Remote Similarity	NPC27408
0.5625	Remote Similarity	NPC476185
0.5593	Remote Similarity	NPC18260
0.5593	Remote Similarity	NPC483773
0.5556	Remote Similarity	NPC181712
0.5536	Remote Similarity	NPC130230
0.5517	Remote Similarity	NPC226973
0.55	Remote Similarity	NPC303644
0.55	Remote Similarity	NPC64051
0.5493	Remote Similarity	NPC19709
0.5484	Remote Similarity	NPC47781
0.5467	Remote Similarity	NPC311830
0.5455	Remote Similarity	NPC31872
0.5443	Remote Similarity	NPC65003
0.5429	Remote Similarity	NPC71061
0.5429	Remote Similarity	NPC72425
0.5424	Remote Similarity	NPC306821
0.5424	Remote Similarity	NPC156222
0.5424	Remote Similarity	NPC187498
0.5417	Remote Similarity	NPC189142
0.5417	Remote Similarity	NPC77660
0.5417	Remote Similarity	NPC601565
0.541	Remote Similarity	NPC200740
0.541	Remote Similarity	NPC270620
0.541	Remote Similarity	NPC166753
0.5385	Remote Similarity	NPC110969
0.5375	Remote Similarity	NPC122809
0.5333	Remote Similarity	NPC100887
0.5333	Remote Similarity	NPC184136
0.5333	Remote Similarity	NPC62536
0.5333	Remote Similarity	NPC76376
0.5333	Remote Similarity	NPC80188
0.5333	Remote Similarity	NPC120464
0.5333	Remote Similarity	NPC266597
0.5333	Remote Similarity	NPC601901
0.5333	Remote Similarity	NPC604085
0.5333	Remote Similarity	NPC605755
0.5333	Remote Similarity	NPC608742
0.5323	Remote Similarity	NPC58382
0.5323	Remote Similarity	NPC236769
0.5323	Remote Similarity	NPC52005
0.5323	Remote Similarity	NPC12200
0.5323	Remote Similarity	NPC206604
0.5312	Remote Similarity	NPC605587
0.5309	Remote Similarity	NPC485523
0.5309	Remote Similarity	NPC485524
0.5301	Remote Similarity	NPC270675
0.5301	Remote Similarity	NPC195685
0.5263	Remote Similarity	NPC222713
0.5263	Remote Similarity	NPC220169
0.5263	Remote Similarity	NPC296197
0.5263	Remote Similarity	NPC607707
0.5254	Remote Similarity	NPC293183
0.5254	Remote Similarity	NPC75279
0.5246	Remote Similarity	NPC269652
0.5246	Remote Similarity	NPC605047
0.5227	Remote Similarity	NPC472993
0.5224	Remote Similarity	NPC293852
0.5211	Remote Similarity	NPC303485
0.5205	Remote Similarity	NPC93337
0.52	Remote Similarity	NPC20505
0.5181	Remote Similarity	NPC210961
0.5179	Remote Similarity	NPC172262
0.5179	Remote Similarity	NPC197425
0.5179	Remote Similarity	NPC216318
0.5176	Remote Similarity	NPC101636
0.5176	Remote Similarity	NPC298171
0.5172	Remote Similarity	NPC279121
0.5167	Remote Similarity	NPC90582
0.5167	Remote Similarity	NPC194281
0.5167	Remote Similarity	NPC600177
0.5161	Remote Similarity	NPC69394
0.5161	Remote Similarity	NPC246204
0.5161	Remote Similarity	NPC212678
0.5161	Remote Similarity	NPC83508
0.5143	Remote Similarity	NPC604322
0.5139	Remote Similarity	NPC186227
0.5135	Remote Similarity	NPC46420
0.5135	Remote Similarity	NPC10807
0.5135	Remote Similarity	NPC161881
0.5135	Remote Similarity	NPC105025
0.5132	Remote Similarity	NPC22832
0.5132	Remote Similarity	NPC243930
0.5132	Remote Similarity	NPC601144
0.5116	Remote Similarity	NPC179862
0.5116	Remote Similarity	NPC472994
0.5088	Remote Similarity	NPC22783
0.5088	Remote Similarity	NPC78540
0.5088	Remote Similarity	NPC12367
0.5082	Remote Similarity	NPC22519
0.5082	Remote Similarity	NPC101830
0.5082	Remote Similarity	NPC188203
0.5082	Remote Similarity	NPC276409
0.5082	Remote Similarity	NPC605144
0.5079	Remote Similarity	NPC160951
0.5079	Remote Similarity	NPC283600
0.5079	Remote Similarity	NPC606638
0.5068	Remote Similarity	NPC261866
0.5062	Remote Similarity	NPC22062
0.5062	Remote Similarity	NPC473634
0.5062	Remote Similarity	NPC138811

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604328 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5612
0.1-0.2	3434
0.2-0.3	89
0.3-0.4	12
0.4-0.5	2
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
0.5172	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