NPASS Compound

Natural Product: NPC611516

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 99104 0 0 0 0 0 0 0 0999 V2000 -7.7644 1.8897 2.1737 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1051 1.6441 0.8269 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.8468 0.5342 0.0684 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1829 0.4217 -1.2578 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7158 0.1429 -1.2383 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1935 0.6534 -2.5303 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3212 1.5429 -2.5165 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6251 0.1927 -3.7625 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3999 -1.3347 -1.2355 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9102 -1.4896 -1.2172 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2601 -0.9750 0.0580 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8729 -1.5854 1.2937 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5962 0.4579 -0.0069 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6749 1.3674 0.0220 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2499 0.9749 0.1220 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0410 -0.2784 -0.7147 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4396 -0.5274 -0.8403 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8369 -1.7663 -1.5298 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0543 0.5658 -1.7131 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5309 0.6434 -1.6521 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8624 1.9218 -2.1948 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1861 0.5195 -0.3194 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5046 0.0047 -0.3970 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6208 0.7347 -0.0213 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4143 1.8792 0.3940 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9796 0.2012 -0.1031 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9825 0.9466 0.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3811 0.5904 0.2587 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3397 1.4856 0.6893 C 0 0 0 0 0 0 0 0 0 0 0 0 11.6880 1.1819 0.6913 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1251 -0.0510 0.2537 C 0 0 0 0 0 0 0 0 0 0 0 0 13.4790 -0.4092 0.2350 O 0 0 0 0 0 0 0 0 0 0 0 0 11.1860 -0.9564 -0.1790 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8235 -0.6269 -0.1723 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4752 -0.3757 0.6721 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1011 -1.7109 0.8195 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7730 0.2667 2.0567 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9902 -0.3155 0.5416 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2859 -1.1636 1.5091 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1653 -1.3490 1.4350 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8009 -1.3089 0.0645 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7225 -2.7333 -0.4557 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0077 0.9042 -0.1330 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7455 0.9943 1.1512 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0451 2.0137 2.0282 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5086 1.0874 2.9028 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3759 2.8451 2.5729 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8651 1.9466 2.0722 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9997 2.5563 0.2435 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6628 -0.3894 0.6330 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9003 0.7732 -0.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6762 -0.3439 -1.9001 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3605 1.3929 -1.8080 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6172 0.7771 -4.5976 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9711 -1.9383 -0.5468 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7131 -1.6887 -2.2667 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6437 -2.4638 -1.5623 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5319 -0.7851 -2.0255 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9003 -1.9698 1.1488 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3189 -2.4626 1.6952 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8086 -0.8313 2.1051 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9246 2.4594 -0.0254 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0914 0.8266 1.2082 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6630 1.8469 -0.1730 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4352 -0.0929 -1.7158 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2528 -1.8024 -2.4944 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8920 -2.6978 -1.0117 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8937 -1.6285 -1.9200 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8022 0.2583 -2.7777 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6249 1.5459 -1.6180 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0078 -0.0337 -2.4250 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5206 1.9428 -3.1396 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2816 1.5532 0.0882 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1864 -0.7942 -0.4635 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7165 1.9596 0.6321 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0014 2.4659 1.0384 H 0 0 0 0 0 0 0 0 0 0 0 0 12.4512 1.8788 1.0281 H 0 0 0 0 0 0 0 0 0 0 0 0 14.2005 0.1946 0.5754 H 0 0 0 0 0 0 0 0 0 0 0 0 11.5341 -1.9213 -0.5212 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1004 -1.3518 -0.5168 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2122 -1.5269 0.9197 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9955 -2.4425 0.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8507 -2.2126 1.7945 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8504 0.4827 2.1537 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2349 1.2327 2.0691 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4787 -0.4255 2.8663 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8191 0.8016 0.7157 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5016 -0.7489 2.5438 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8491 -2.1489 1.5271 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7745 -0.7559 2.1437 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3312 -2.3991 1.8537 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9809 -3.3531 0.1478 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6591 -2.8491 -1.5205 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6509 -3.3242 -0.1546 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0350 1.9747 -0.5286 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9932 0.0755 1.6640 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9859 1.7492 2.1353 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5050 1.9907 3.0354 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1876 3.0460 1.6296 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 6 6 7 2 0 6 8 1 0 5 9 1 0 9 10 1 0 10 11 1 0 11 12 1 1 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 6 17 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 24 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 30 31 2 0 31 32 1 0 31 33 1 0 33 34 2 0 22 35 1 0 35 36 1 0 35 37 1 0 35 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 6 13 43 1 0 43 44 1 0 44 45 1 0 44 2 1 0 43 5 1 0 41 11 1 0 41 16 1 0 38 17 1 0 34 28 1 0 1 46 1 0 1 47 1 0 1 48 1 0 2 49 1 6 3 50 1 0 3 51 1 0 4 52 1 0 4 53 1 0 8 54 1 0 9 55 1 0 9 56 1 0 10 57 1 0 10 58 1 0 12 59 1 0 12 60 1 0 12 61 1 0 14 62 1 0 15 63 1 0 15 64 1 0 16 65 1 0 18 66 1 0 18 67 1 0 18 68 1 0 19 69 1 0 19 70 1 0 20 71 1 6 21 72 1 0 22 73 1 1 26 74 1 0 27 75 1 0 29 76 1 0 30 77 1 0 32 78 1 0 33 79 1 0 34 80 1 0 36 81 1 0 36 82 1 0 36 83 1 0 37 84 1 0 37 85 1 0 37 86 1 0 38 87 1 1 39 88 1 0 39 89 1 0 40 90 1 0 40 91 1 0 42 92 1 0 42 93 1 0 42 94 1 0 43 95 1 0 44 96 1 1 45 97 1 0 45 98 1 0 45 99 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 NPC611516 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	7732
0.1-0.2	36518
0.2-0.3	4869
0.3-0.4	546
0.4-0.5	114
0.5-0.6	43
0.6-0.7	15
0.7-0.8	0
0.8-0.85	3
0.85-0.9	1
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC304110
1.0	High Similarity	NPC27518
0.9186	High Similarity	NPC178093
0.8587	High Similarity	NPC118033
0.8352	Intermediate Similarity	NPC479745
0.8222	Intermediate Similarity	NPC25491
0.8111	Intermediate Similarity	NPC605663
0.7849	Intermediate Similarity	NPC324798
0.7849	Intermediate Similarity	NPC479742
0.7717	Intermediate Similarity	NPC479744
0.7474	Intermediate Similarity	NPC482051
0.7381	Intermediate Similarity	NPC230151
0.7368	Intermediate Similarity	NPC479747
0.7368	Intermediate Similarity	NPC479746
0.71	Intermediate Similarity	NPC481234
0.71	Intermediate Similarity	NPC479431
0.7021	Intermediate Similarity	NPC171007
0.7021	Intermediate Similarity	NPC190849
0.7	Intermediate Similarity	NPC601567
0.7	Intermediate Similarity	NPC606631
0.6979	Remote Similarity	NPC172311
0.6957	Remote Similarity	NPC485587
0.6882	Remote Similarity	NPC173569
0.6667	Remote Similarity	NPC479739
0.6633	Remote Similarity	NPC482052
0.6598	Remote Similarity	NPC101863
0.6471	Remote Similarity	NPC479740
0.6471	Remote Similarity	NPC479741
0.6465	Remote Similarity	NPC54627
0.6465	Remote Similarity	NPC249817
0.6429	Remote Similarity	NPC22676
0.6337	Remote Similarity	NPC475482
0.6061	Remote Similarity	NPC477874
0.6019	Remote Similarity	NPC482049
0.6019	Remote Similarity	NPC482050
0.5978	Remote Similarity	NPC233012
0.5882	Remote Similarity	NPC198621
0.5882	Remote Similarity	NPC216940
0.5843	Remote Similarity	NPC485589
0.5761	Remote Similarity	NPC485588
0.5686	Remote Similarity	NPC475457
0.566	Remote Similarity	NPC610795
0.5644	Remote Similarity	NPC475138
0.5625	Remote Similarity	NPC485585
0.5619	Remote Similarity	NPC132126
0.5612	Remote Similarity	NPC485882
0.5596	Remote Similarity	NPC310729
0.5596	Remote Similarity	NPC150310
0.5591	Remote Similarity	NPC485586
0.5586	Remote Similarity	NPC481235
0.5524	Remote Similarity	NPC488214
0.5481	Remote Similarity	NPC477873
0.5444	Remote Similarity	NPC71074
0.5444	Remote Similarity	NPC605937
0.5385	Remote Similarity	NPC32407
0.5385	Remote Similarity	NPC263548
0.5385	Remote Similarity	NPC606320
0.5333	Remote Similarity	NPC51700
0.5333	Remote Similarity	NPC488215
0.5333	Remote Similarity	NPC88716
0.5333	Remote Similarity	NPC68160
0.5283	Remote Similarity	NPC262970
0.5243	Remote Similarity	NPC182249
0.5243	Remote Similarity	NPC473591
0.5243	Remote Similarity	NPC248287
0.5243	Remote Similarity	NPC234548
0.5217	Remote Similarity	NPC173089
0.5217	Remote Similarity	NPC87095
0.5143	Remote Similarity	NPC26045
0.5109	Remote Similarity	NPC61543
0.5109	Remote Similarity	NPC293048
0.5109	Remote Similarity	NPC225585
0.5098	Remote Similarity	NPC177246
0.5098	Remote Similarity	NPC470617
0.5098	Remote Similarity	NPC470616
0.5045	Remote Similarity	NPC475454
0.5045	Remote Similarity	NPC473579
0.5043	Remote Similarity	NPC53520

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611516 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3678
0.1-0.2	5378
0.2-0.3	87
0.3-0.4	6
0.4-0.5	1
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