NPASS Compound

Natural Product: NPC602579

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 72 76 0 0 0 0 0 0 0 0999 V2000 -5.7063 1.9575 2.9529 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0962 0.5717 2.9523 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2464 0.3707 1.8825 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8868 0.2323 0.6671 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9165 -0.0931 -0.2800 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7617 0.8885 -1.2446 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6726 0.3815 -2.1973 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5273 0.2108 -1.4186 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4278 -0.1473 -2.2052 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6508 -0.3180 -1.3396 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8695 0.3147 -1.3894 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1890 1.2377 -2.3498 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4385 1.8495 -2.3546 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7283 2.7752 -3.3365 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3520 1.5114 -1.3754 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5903 2.1216 -1.3849 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8883 2.9648 -2.2585 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4744 1.7442 -0.3742 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1266 0.8159 0.5757 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0428 0.3958 1.6596 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3105 0.8970 1.8025 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1344 0.4643 2.8471 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6741 -0.4737 3.7438 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4598 -0.9363 4.8023 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4042 -0.9904 3.6190 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9178 -1.9402 4.5145 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6162 -0.5479 2.5840 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9548 0.2792 0.5337 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0597 0.5843 -0.3933 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8220 -0.0050 -0.4097 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6621 -1.4971 -2.8739 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4191 -1.7898 -3.6750 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9278 -1.3820 -3.6971 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2114 -2.5899 -4.3332 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0355 -0.9835 -2.7364 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2845 -1.0174 -3.3272 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9377 -0.8246 0.6514 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1954 -0.3096 0.2599 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0489 -1.5259 1.9900 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1423 -2.3632 1.9480 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1460 -0.5039 3.1016 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0103 -1.1896 4.3069 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3801 2.5739 3.8161 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8098 1.8801 3.0365 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3791 2.5096 2.0474 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4541 0.5228 3.8710 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3373 1.2397 0.4347 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4739 1.8218 -0.7651 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6897 1.0679 -1.8153 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5240 1.0585 -3.0456 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2413 0.5806 -2.9933 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4929 1.5031 -3.1057 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3230 2.7179 -4.2714 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4425 2.2043 -0.3605 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6636 1.6283 1.1001 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1232 0.8633 2.9483 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4577 -0.7545 4.8066 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3944 -2.8230 4.6702 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6022 -0.9548 2.4774 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5608 -0.7228 0.3294 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8474 -2.2342 -2.0703 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6997 -2.7434 -3.5646 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8354 -0.5498 -4.4295 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5344 -2.3517 -5.2489 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9679 -1.6868 -1.8665 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9387 -1.2738 -2.6429 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7073 -1.6122 -0.0953 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9934 0.2943 -0.5058 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1412 -2.1489 2.1069 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8632 -1.9243 1.4137 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1342 -0.0115 3.0258 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7870 -1.8145 4.3493 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 2 0 19 28 1 0 28 29 1 0 29 30 2 0 9 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 4 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 39 41 1 0 41 42 1 0 41 2 1 0 35 7 1 0 30 11 1 0 29 15 1 0 27 20 1 0 1 43 1 0 1 44 1 0 1 45 1 0 2 46 1 1 4 47 1 6 6 48 1 0 6 49 1 0 7 50 1 6 9 51 1 6 12 52 1 0 14 53 1 0 18 54 1 0 21 55 1 0 22 56 1 0 24 57 1 0 26 58 1 0 27 59 1 0 30 60 1 0 31 61 1 1 32 62 1 0 33 63 1 6 34 64 1 0 35 65 1 1 36 66 1 0 37 67 1 6 38 68 1 0 39 69 1 1 40 70 1 0 41 71 1 1 42 72 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 NPC602579 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	21540
0.1-0.2	24517
0.2-0.3	2794
0.3-0.4	539
0.4-0.5	285
0.5-0.6	112
0.6-0.7	50
0.7-0.8	1
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC210073
0.8875	High Similarity	NPC44931
0.8353	Intermediate Similarity	NPC209296
0.8313	Intermediate Similarity	NPC22062
0.8313	Intermediate Similarity	NPC473634
0.8313	Intermediate Similarity	NPC138811
0.8193	Intermediate Similarity	NPC67105
0.8182	Intermediate Similarity	NPC19709
0.8023	Intermediate Similarity	NPC65711
0.7386	Intermediate Similarity	NPC186816
0.7356	Intermediate Similarity	NPC227508
0.7333	Intermediate Similarity	NPC229409
0.7294	Intermediate Similarity	NPC190003
0.7283	Intermediate Similarity	NPC101636
0.7195	Intermediate Similarity	NPC189142
0.7195	Intermediate Similarity	NPC77660
0.716	Intermediate Similarity	NPC473043
0.716	Intermediate Similarity	NPC331652
0.7	Intermediate Similarity	NPC115674
0.6957	Remote Similarity	NPC473623
0.6882	Remote Similarity	NPC488089
0.6813	Remote Similarity	NPC204693
0.6737	Remote Similarity	NPC298171
0.6701	Remote Similarity	NPC11468
0.6667	Remote Similarity	NPC480441
0.6667	Remote Similarity	NPC238376
0.6559	Remote Similarity	NPC64051
0.6556	Remote Similarity	NPC254540
0.6522	Remote Similarity	NPC203259
0.6522	Remote Similarity	NPC33054
0.6522	Remote Similarity	NPC176740
0.6522	Remote Similarity	NPC471725
0.6522	Remote Similarity	NPC134532
0.6522	Remote Similarity	NPC602582
0.6489	Remote Similarity	NPC470443
0.6413	Remote Similarity	NPC275454
0.6374	Remote Similarity	NPC8856
0.6354	Remote Similarity	NPC270675
0.6354	Remote Similarity	NPC195685
0.6346	Remote Similarity	NPC298666
0.6346	Remote Similarity	NPC198199
0.6344	Remote Similarity	NPC303913
0.6337	Remote Similarity	NPC473644
0.6322	Remote Similarity	NPC271692
0.6289	Remote Similarity	NPC473073
0.6279	Remote Similarity	NPC39360
0.6279	Remote Similarity	NPC29763
0.6279	Remote Similarity	NPC210003
0.6275	Remote Similarity	NPC311850
0.625	Remote Similarity	NPC27942
0.6211	Remote Similarity	NPC46202
0.6211	Remote Similarity	NPC126784
0.6211	Remote Similarity	NPC241423
0.6211	Remote Similarity	NPC475366
0.6176	Remote Similarity	NPC25523
0.617	Remote Similarity	NPC65003
0.6168	Remote Similarity	NPC120952
0.6162	Remote Similarity	NPC472994
0.6095	Remote Similarity	NPC68592
0.6064	Remote Similarity	NPC173582
0.6064	Remote Similarity	NPC265885
0.6064	Remote Similarity	NPC181465
0.6064	Remote Similarity	NPC215710
0.6064	Remote Similarity	NPC473438
0.6064	Remote Similarity	NPC253788
0.6044	Remote Similarity	NPC605784
0.602	Remote Similarity	NPC142142
0.6	Remote Similarity	NPC473512
0.6	Remote Similarity	NPC20505
0.596	Remote Similarity	NPC475382
0.5955	Remote Similarity	NPC181712
0.5941	Remote Similarity	NPC14187
0.5934	Remote Similarity	NPC22832
0.5934	Remote Similarity	NPC601144
0.5922	Remote Similarity	NPC472993
0.5909	Remote Similarity	NPC261866
0.5909	Remote Similarity	NPC249281
0.5909	Remote Similarity	NPC108831
0.5909	Remote Similarity	NPC182634
0.5895	Remote Similarity	NPC39834
0.587	Remote Similarity	NPC311830
0.5843	Remote Similarity	NPC95090
0.5843	Remote Similarity	NPC277205
0.5843	Remote Similarity	NPC27408
0.5843	Remote Similarity	NPC37919
0.5833	Remote Similarity	NPC129827
0.5833	Remote Similarity	NPC65563
0.5833	Remote Similarity	NPC470949
0.5806	Remote Similarity	NPC276377
0.58	Remote Similarity	NPC195257
0.5794	Remote Similarity	NPC488086
0.5789	Remote Similarity	NPC187379
0.5778	Remote Similarity	NPC46420
0.5769	Remote Similarity	NPC108406
0.5766	Remote Similarity	NPC262222
0.5755	Remote Similarity	NPC488087
0.5745	Remote Similarity	NPC172807
0.567	Remote Similarity	NPC156869
0.5667	Remote Similarity	NPC158674
0.5667	Remote Similarity	NPC136042
0.5644	Remote Similarity	NPC476472
0.5644	Remote Similarity	NPC294815
0.5644	Remote Similarity	NPC16194
0.5612	Remote Similarity	NPC473571
0.5612	Remote Similarity	NPC110941
0.5607	Remote Similarity	NPC488083
0.5604	Remote Similarity	NPC58716
0.5604	Remote Similarity	NPC84362
0.5604	Remote Similarity	NPC45638
0.56	Remote Similarity	NPC483707
0.5591	Remote Similarity	NPC243930
0.5579	Remote Similarity	NPC211594
0.5567	Remote Similarity	NPC67326
0.5545	Remote Similarity	NPC486577
0.5543	Remote Similarity	NPC201292
0.5534	Remote Similarity	NPC484301
0.5534	Remote Similarity	NPC253685
0.5534	Remote Similarity	NPC135358
0.5532	Remote Similarity	NPC116458
0.5532	Remote Similarity	NPC246943
0.5532	Remote Similarity	NPC607707
0.5521	Remote Similarity	NPC606546
0.551	Remote Similarity	NPC479405
0.551	Remote Similarity	NPC150164
0.5495	Remote Similarity	NPC168822
0.5464	Remote Similarity	NPC473657
0.5455	Remote Similarity	NPC479404
0.5446	Remote Similarity	NPC122467
0.5446	Remote Similarity	NPC32641
0.5446	Remote Similarity	NPC256188
0.5446	Remote Similarity	NPC473327
0.5426	Remote Similarity	NPC181616
0.54	Remote Similarity	NPC488073
0.5368	Remote Similarity	NPC99957
0.5354	Remote Similarity	NPC218488
0.5347	Remote Similarity	NPC479403
0.534	Remote Similarity	NPC80068
0.534	Remote Similarity	NPC89127
0.5327	Remote Similarity	NPC292019
0.5327	Remote Similarity	NPC202908
0.5319	Remote Similarity	NPC282169
0.5319	Remote Similarity	NPC611303
0.5306	Remote Similarity	NPC295613
0.5294	Remote Similarity	NPC72016
0.5294	Remote Similarity	NPC35119
0.5258	Remote Similarity	NPC116864
0.5258	Remote Similarity	NPC244776
0.5248	Remote Similarity	NPC475497
0.5248	Remote Similarity	NPC488074
0.52	Remote Similarity	NPC233994
0.5161	Remote Similarity	NPC297987
0.5161	Remote Similarity	NPC323593
0.5161	Remote Similarity	NPC203500
0.5152	Remote Similarity	NPC471079
0.5146	Remote Similarity	NPC150767
0.514	Remote Similarity	NPC121703
0.5135	Remote Similarity	NPC488088
0.5106	Remote Similarity	NPC27640
0.5102	Remote Similarity	NPC294629
0.5102	Remote Similarity	NPC131407
0.51	Remote Similarity	NPC15358
0.5098	Remote Similarity	NPC284277
0.5098	Remote Similarity	NPC240306
0.5094	Remote Similarity	NPC470446
0.5094	Remote Similarity	NPC179862
0.5054	Remote Similarity	NPC127546
0.5054	Remote Similarity	NPC57625
0.5054	Remote Similarity	NPC173637
0.5054	Remote Similarity	NPC317489
0.5054	Remote Similarity	NPC223424
0.5054	Remote Similarity	NPC600591
0.5053	Remote Similarity	NPC59534
0.5051	Remote Similarity	NPC251417
0.505	Remote Similarity	NPC3583
0.505	Remote Similarity	NPC607513
0.5049	Remote Similarity	NPC12013
0.5049	Remote Similarity	NPC211532
0.5049	Remote Similarity	NPC11432
0.5049	Remote Similarity	NPC488364
0.5049	Remote Similarity	NPC477613
0.5048	Remote Similarity	NPC477629

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602579 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5398
0.1-0.2	3687
0.2-0.3	55
0.3-0.4	4
0.4-0.5	1
0.5-0.6	0
0.6-0.7	3
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8353	Intermediate Similarity	NPD7054	Phase 4
0.7363	Intermediate Similarity	NPD7251	Phase 2
0.6522	Remote Similarity	NPD6797	Phase 2
0.62	Remote Similarity	NPD7472	Pre-clinical
0.62	Remote Similarity	NPD7808	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