NPASS Compound

Natural Product: NPC606857

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 82 85 0 0 0 0 0 0 0 0999 V2000 3.8230 2.4823 0.1654 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8605 1.2522 0.1427 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3413 0.4713 -1.0490 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7667 0.0357 -0.9423 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0724 -0.8486 0.2254 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3603 -2.0260 0.2320 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5543 -1.1987 0.0968 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8499 -1.9455 -1.1595 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2815 -0.0100 0.0900 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0311 -1.9965 1.2894 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3831 -3.2014 1.4057 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4754 1.7743 0.0463 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1872 2.5689 -1.2027 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0060 1.7896 -1.8217 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7524 1.5278 -0.5875 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2044 2.8241 0.0096 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8227 0.5182 -0.6270 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2465 -0.1142 -1.6878 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3400 -1.1004 -1.5245 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3599 -0.4326 -0.5918 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6895 -1.1072 -0.6521 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4101 -0.5632 -1.8935 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6053 -2.6055 -0.7794 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4776 -0.6840 0.5272 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3730 -1.3542 0.9666 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1386 0.6052 1.1709 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6791 0.7145 1.5388 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8090 -0.2873 0.7890 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7637 -1.5963 1.5444 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4241 0.2473 0.6846 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6649 0.5040 1.7505 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2803 1.0346 1.6937 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3362 0.8972 0.3131 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4722 -0.5608 0.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7900 2.1910 0.6085 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8840 2.9375 -0.8233 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3641 3.2227 0.8529 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0066 0.7591 1.1102 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7446 -0.4404 -1.1561 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2805 1.1420 -1.9313 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4386 0.9192 -0.8728 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 -0.5093 -1.8563 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9571 -0.3549 1.2070 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1373 -2.3928 -0.6379 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6434 -2.7010 -0.9930 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9315 -2.3911 -1.6087 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2346 -1.2335 -1.9172 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4002 0.3631 0.9982 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9872 -1.3799 2.2157 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1087 -2.1966 1.1143 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7181 -3.1338 2.1150 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4106 2.5854 0.8808 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0034 2.7057 -1.8895 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7723 3.5725 -0.9883 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3542 0.8321 -2.2507 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5108 2.3990 -2.5847 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5063 3.5046 -0.8239 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1047 2.7214 0.6506 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4529 3.3602 0.6043 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7803 0.1111 -2.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8373 -1.3675 -2.4652 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9257 -1.9599 -0.9738 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4839 0.5996 -1.0055 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5038 -0.5408 -1.7497 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2110 -1.2155 -2.7666 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0830 0.4827 -2.0971 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4176 -3.0272 -0.1281 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8736 -2.9216 -1.8158 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6203 -3.0210 -0.5666 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7757 0.8157 2.0572 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3865 1.4004 0.4071 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5381 0.6075 2.6433 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3259 1.7357 1.2497 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0044 -2.2312 1.0498 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4163 -1.3626 2.5696 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7486 -2.0498 1.6252 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0655 0.3199 2.7438 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1976 2.0477 2.1200 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3361 0.3817 2.3684 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3907 -1.1022 0.5606 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4643 -0.8740 -0.9876 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3496 -0.9256 0.6323 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 5 7 1 0 7 8 1 0 7 9 1 6 7 10 1 0 10 11 1 0 2 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 1 15 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 21 24 1 0 24 25 2 0 24 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 28 30 1 0 30 31 2 0 31 32 1 0 32 33 1 0 33 34 1 6 33 12 1 0 33 15 1 0 30 17 1 0 28 20 1 0 1 35 1 0 1 36 1 0 1 37 1 0 2 38 1 1 3 39 1 0 3 40 1 0 4 41 1 0 4 42 1 0 5 43 1 1 6 44 1 0 8 45 1 0 8 46 1 0 8 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 11 51 1 0 12 52 1 1 13 53 1 0 13 54 1 0 14 55 1 0 14 56 1 0 16 57 1 0 16 58 1 0 16 59 1 0 18 60 1 0 19 61 1 0 19 62 1 0 20 63 1 6 22 64 1 0 22 65 1 0 22 66 1 0 23 67 1 0 23 68 1 0 23 69 1 0 26 70 1 0 26 71 1 0 27 72 1 0 27 73 1 0 29 74 1 0 29 75 1 0 29 76 1 0 31 77 1 0 32 78 1 0 32 79 1 0 34 80 1 0 34 81 1 0 34 82 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 NPC606857 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	20786
0.1-0.2	24983
0.2-0.3	3719
0.3-0.4	286
0.4-0.5	48
0.5-0.6	28
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
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	NPC44181
0.8793	High Similarity	NPC89077
0.7302	Intermediate Similarity	NPC4166
0.7302	Intermediate Similarity	NPC311092
0.6719	Remote Similarity	NPC170793
0.6471	Remote Similarity	NPC87552
0.6176	Remote Similarity	NPC470048
0.6154	Remote Similarity	NPC6707
0.5921	Remote Similarity	NPC484794
0.5556	Remote Similarity	NPC472942
0.5556	Remote Similarity	NPC69622
0.5556	Remote Similarity	NPC607637
0.5484	Remote Similarity	NPC603740
0.5484	Remote Similarity	NPC607298
0.5441	Remote Similarity	NPC479660
0.5429	Remote Similarity	NPC99909
0.5395	Remote Similarity	NPC478312
0.5385	Remote Similarity	NPC484796
0.5352	Remote Similarity	NPC475772
0.5352	Remote Similarity	NPC260992
0.5342	Remote Similarity	NPC250575
0.5312	Remote Similarity	NPC605557
0.5294	Remote Similarity	NPC205455
0.5286	Remote Similarity	NPC202389
0.5278	Remote Similarity	NPC83569
0.5195	Remote Similarity	NPC285702
0.5195	Remote Similarity	NPC166745
0.5195	Remote Similarity	NPC235464
0.5152	Remote Similarity	NPC472936
0.5135	Remote Similarity	NPC69279
0.5104	Remote Similarity	NPC488417
0.5104	Remote Similarity	NPC610721
0.5067	Remote Similarity	NPC66429
0.5065	Remote Similarity	NPC155676
0.5051	Remote Similarity	NPC488418
0.5051	Remote Similarity	NPC610358

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606857 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7316
0.1-0.2	1702
0.2-0.3	131
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
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
		NPD

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