NPASS Compound

Natural Product: NPC605742

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 87 92 0 0 0 0 0 0 0 0999 V2000 9.4812 -1.5231 -0.7212 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1680 -1.6244 -1.2225 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1934 -0.7724 -0.7244 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4495 0.1640 0.2370 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4431 1.0305 0.7398 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1880 0.9229 0.2485 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8886 -0.0258 -0.7391 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8805 -0.8826 -1.2374 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6695 -1.7869 -2.1576 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2564 -2.6003 -3.0615 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1357 1.8087 0.7737 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2860 1.2500 1.8433 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5432 0.0285 1.3666 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1629 -1.1740 1.4712 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5048 -2.3012 1.0658 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2074 -2.2082 0.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 -3.4508 0.1740 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5344 -1.0377 0.4223 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6795 -0.8269 -0.0420 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9880 -0.9948 0.0786 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7703 0.1988 0.3168 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1085 0.1915 0.4634 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7574 -1.0245 0.3800 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0456 -2.1808 0.1524 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6555 -2.1819 -0.0021 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0388 -3.4019 -0.2344 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7920 -4.5831 -0.3148 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2299 -1.0159 0.5594 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5635 0.0170 1.5924 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0436 1.3183 1.4001 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.1234 2.1408 2.5964 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8193 1.4660 0.7035 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0056 2.2937 -0.5548 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8101 1.5999 -1.5955 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1876 0.7651 -2.5171 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9089 0.1150 -3.4825 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2874 0.2567 -3.5889 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0227 -0.4123 -4.5835 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8722 1.0927 -2.6588 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1693 1.7483 -1.6892 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2863 0.1006 0.8655 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7081 3.0849 1.1034 N 0 0 0 0 0 0 0 0 0 0 0 0 3.6962 3.9792 1.6330 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7383 2.9403 2.1036 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8372 2.0024 1.7706 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5156 -1.3966 0.3642 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9894 -0.6223 -1.1736 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1166 -2.3786 -1.0734 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4450 0.2846 0.6595 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9072 -0.1132 -1.1280 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4522 -3.6938 -2.7607 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7245 -2.5563 -4.0944 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1492 -2.6506 -3.3067 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4585 2.0165 -0.1096 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4973 1.9838 2.0858 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8217 1.0319 2.7906 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1613 -1.3169 1.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9687 -3.2746 1.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4660 -4.0744 0.9613 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1978 1.1324 0.3715 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5769 -3.1436 0.0870 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3930 -4.5030 -1.2662 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4182 -4.7985 0.5672 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0860 -5.4372 -0.5308 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7882 -0.7784 -0.3706 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5698 -2.0330 0.9388 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6754 0.0051 1.6954 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2076 -0.3209 2.6128 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2718 1.8929 3.2965 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0840 1.9420 3.1106 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0743 3.2154 2.3300 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1367 2.0929 1.3506 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4601 3.2719 -0.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9976 2.5202 -0.9988 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0950 0.6364 -2.4540 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4464 -0.5479 -4.2172 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9482 -0.7748 -4.4430 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9616 1.1852 -2.7658 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6758 2.3840 -0.9946 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8100 1.0633 0.7878 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1043 5.0284 1.5767 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4877 3.7607 2.6951 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8074 3.9310 0.9776 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0892 3.9427 2.4420 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1980 2.5298 3.0149 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7317 2.5874 1.4070 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1178 1.4696 2.7227 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 6 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 1 0 23 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 33 34 1 0 34 35 2 0 35 36 1 0 36 37 2 0 37 38 1 0 37 39 1 0 39 40 2 0 18 41 2 0 11 42 1 0 42 43 1 0 42 44 1 0 44 45 1 0 8 3 1 0 41 13 1 0 45 5 1 0 25 20 1 0 40 34 1 0 32 22 1 0 1 46 1 0 1 47 1 0 1 48 1 0 4 49 1 0 7 50 1 0 10 51 1 0 10 52 1 0 10 53 1 0 11 54 1 6 12 55 1 0 12 56 1 0 14 57 1 0 15 58 1 0 17 59 1 0 21 60 1 0 24 61 1 0 27 62 1 0 27 63 1 0 27 64 1 0 28 65 1 0 28 66 1 0 29 67 1 0 29 68 1 0 31 69 1 0 31 70 1 0 31 71 1 0 32 72 1 1 33 73 1 0 33 74 1 0 35 75 1 0 36 76 1 0 38 77 1 0 39 78 1 0 40 79 1 0 41 80 1 0 43 81 1 0 43 82 1 0 43 83 1 0 44 84 1 0 44 85 1 0 45 86 1 0 45 87 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 NPC605742 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	29051
0.1-0.2	18581
0.2-0.3	1882
0.3-0.4	201
0.4-0.5	51
0.5-0.6	46
0.6-0.7	28
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8871	High Similarity	NPC256012
0.8871	High Similarity	NPC610965
0.8615	High Similarity	NPC610959
0.7812	Intermediate Similarity	NPC317272
0.7812	Intermediate Similarity	NPC268503
0.7759	Intermediate Similarity	NPC185838
0.75	Intermediate Similarity	NPC601503
0.726	Intermediate Similarity	NPC223690
0.726	Intermediate Similarity	NPC9532
0.7123	Intermediate Similarity	NPC600054
0.7123	Intermediate Similarity	NPC601504
0.7067	Intermediate Similarity	NPC290005
0.7042	Intermediate Similarity	NPC240841
0.7027	Intermediate Similarity	NPC185639
0.7027	Intermediate Similarity	NPC251735
0.7027	Intermediate Similarity	NPC49075
0.7027	Intermediate Similarity	NPC599951
0.6857	Remote Similarity	NPC480592
0.6842	Remote Similarity	NPC181796
0.6842	Remote Similarity	NPC54654
0.6842	Remote Similarity	NPC7715
0.6842	Remote Similarity	NPC328155
0.6842	Remote Similarity	NPC222661
0.6842	Remote Similarity	NPC285931
0.6712	Remote Similarity	NPC480591
0.6667	Remote Similarity	NPC212237
0.6582	Remote Similarity	NPC24260
0.6582	Remote Similarity	NPC611658
0.6494	Remote Similarity	NPC274716
0.6494	Remote Similarity	NPC167116
0.6494	Remote Similarity	NPC609821
0.6456	Remote Similarity	NPC601489
0.6456	Remote Similarity	NPC604804
0.6406	Remote Similarity	NPC191376
0.6375	Remote Similarity	NPC605743
0.6308	Remote Similarity	NPC321505
0.6308	Remote Similarity	NPC179825
0.6269	Remote Similarity	NPC247639
0.6269	Remote Similarity	NPC25084
0.6265	Remote Similarity	NPC206900
0.6216	Remote Similarity	NPC603603
0.6061	Remote Similarity	NPC135538
0.6061	Remote Similarity	NPC24233
0.6047	Remote Similarity	NPC41122
0.6047	Remote Similarity	NPC318805
0.5968	Remote Similarity	NPC314682
0.5897	Remote Similarity	NPC608819
0.5873	Remote Similarity	NPC213206
0.5873	Remote Similarity	NPC188163
0.5873	Remote Similarity	NPC328750
0.5823	Remote Similarity	NPC311973
0.5823	Remote Similarity	NPC239824
0.5769	Remote Similarity	NPC290582
0.5769	Remote Similarity	NPC217748
0.5769	Remote Similarity	NPC182052
0.5769	Remote Similarity	NPC271013
0.5769	Remote Similarity	NPC42663
0.5769	Remote Similarity	NPC15414
0.573	Remote Similarity	NPC201508
0.5696	Remote Similarity	NPC279228
0.5625	Remote Similarity	NPC600872
0.5556	Remote Similarity	NPC254441
0.5556	Remote Similarity	NPC116465
0.5526	Remote Similarity	NPC76682
0.5526	Remote Similarity	NPC10908
0.5526	Remote Similarity	NPC63646
0.5526	Remote Similarity	NPC317145
0.5526	Remote Similarity	NPC198498
0.5526	Remote Similarity	NPC115284
0.5455	Remote Similarity	NPC276890
0.5444	Remote Similarity	NPC60295
0.5441	Remote Similarity	NPC103379
0.5412	Remote Similarity	NPC8836
0.5402	Remote Similarity	NPC480586
0.5357	Remote Similarity	NPC16357
0.5357	Remote Similarity	NPC302245
0.525	Remote Similarity	NPC603853
0.5244	Remote Similarity	NPC286119
0.5233	Remote Similarity	NPC275680
0.5233	Remote Similarity	NPC22115
0.5227	Remote Similarity	NPC480590
0.5185	Remote Similarity	NPC73492
0.5185	Remote Similarity	NPC299990
0.5185	Remote Similarity	NPC480587
0.5132	Remote Similarity	NPC30779
0.5125	Remote Similarity	NPC12424
0.5125	Remote Similarity	NPC129518
0.5125	Remote Similarity	NPC251580
0.5122	Remote Similarity	NPC609914
0.5077	Remote Similarity	NPC484289
0.5054	Remote Similarity	NPC175890

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605742 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4877
0.1-0.2	4109
0.2-0.3	143
0.3-0.4	13
0.4-0.5	2
0.5-0.6	4
0.6-0.7	2
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
0.6163	Remote Similarity	NPD8053	Approved
0.6092	Remote Similarity	NPD8054	Phase 4
0.5873	Remote Similarity	NPD4664	Clinical (unspecified phase)
0.5526	Remote Similarity	NPD8099	Discontinued
0.525	Remote Similarity	NPD8156	Discontinued
0.5185	Remote Similarity	NPD8095	Phase 1

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