NPASS Compound

Natural Product: NPC590468

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 92 98 0 0 0 0 0 0 0 0999 V2000 3.0151 7.4199 -0.4741 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0525 6.0390 -0.2928 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9989 5.2210 0.0568 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7347 5.7592 0.2675 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2697 4.8754 0.6147 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0538 3.5223 0.7517 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2183 3.0478 0.5305 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2612 3.8747 0.1824 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5504 3.3893 -0.0411 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8416 2.0440 -0.0694 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5251 1.3155 -1.1671 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8161 -0.0441 -1.2016 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4233 -0.6403 -0.1206 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7308 0.1332 0.9799 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4399 1.4727 1.0040 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7257 -2.0856 -0.1708 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6488 -2.9105 0.5196 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3135 -2.5152 0.0640 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5144 -1.5615 0.6552 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2868 -1.2696 0.1266 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1570 -1.9223 -0.9936 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4247 -1.6174 -1.5373 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8431 -2.3047 -2.6827 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6316 -2.8827 -1.5999 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8458 -3.1744 -1.0798 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7005 -4.2208 -1.7079 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4539 -4.9878 -0.6609 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9927 -4.2786 0.4197 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3960 -4.5421 0.6734 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4940 -0.3056 0.7453 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8747 -0.3346 0.6522 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5194 -1.5044 0.9815 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7616 -2.5803 1.3873 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4303 -2.8136 2.7588 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9010 -1.6202 0.9140 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5462 -2.7972 1.2454 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9507 -2.9727 2.5928 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5967 -0.4902 0.4960 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9882 -0.5532 0.4104 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5371 -0.9657 -0.8206 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9410 0.6774 0.1686 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5743 0.7993 0.2332 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8519 2.0482 -0.1120 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1450 2.6002 1.1175 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7526 3.0941 -0.5462 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.0286 3.0310 -1.9655 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0034 3.0772 0.1591 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7471 1.8341 -0.2754 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9727 7.9234 -0.2153 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2091 7.9255 0.0550 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8767 7.6127 -1.5771 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5158 6.8138 0.1722 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2834 5.2206 0.7956 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4438 1.9878 0.6253 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0529 1.7837 -2.0046 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5575 -0.6108 -2.0866 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2070 -0.2934 1.8468 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6991 2.0423 1.8886 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9520 -2.4648 -1.1784 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6946 -2.2073 0.4015 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6818 -2.6700 1.6358 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8876 -1.0570 1.5428 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1011 -2.1662 -3.5211 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7996 -3.4058 -2.4444 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8233 -2.0005 -3.0462 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2367 -3.3833 -2.4977 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0516 -4.9445 -2.2634 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4083 -3.7828 -2.4276 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2403 -5.6139 -1.1430 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7070 -5.7269 -0.2417 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0501 -4.1529 -0.1259 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6472 -4.0772 1.6514 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5014 -5.6513 0.8213 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3240 -2.9505 2.8107 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7107 -1.8927 3.3281 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8942 -3.7214 3.1566 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0694 -3.0759 2.6437 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6309 -2.1312 3.2491 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5160 -3.8896 3.0408 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5322 -1.4417 -0.6759 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8369 -1.6997 -1.2922 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6932 -0.1264 -1.5238 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0932 1.9047 -0.9012 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7621 1.7677 1.7366 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9039 3.1137 1.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9938 3.5109 -2.2265 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2514 3.6162 -2.5364 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0650 1.9783 -2.3357 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5472 4.0051 -0.1079 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8580 2.9838 1.2585 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7824 1.8081 0.1216 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8468 1.7595 -1.3785 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 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 13 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 2 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 20 30 1 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 1 0 32 35 1 0 35 36 1 0 36 37 1 0 35 38 2 0 38 39 1 0 39 40 1 0 38 41 1 0 41 42 2 0 42 43 1 0 43 44 1 0 43 45 1 0 45 46 1 0 45 47 1 0 47 48 1 0 8 3 1 0 15 10 1 0 28 17 1 0 42 31 1 0 44 6 1 0 25 18 1 0 48 41 1 0 1 49 1 0 1 50 1 0 1 51 1 0 4 52 1 0 5 53 1 0 7 54 1 0 11 55 1 0 12 56 1 0 14 57 1 0 15 58 1 0 16 59 1 0 16 60 1 0 17 61 1 1 19 62 1 0 23 63 1 0 23 64 1 0 23 65 1 0 24 66 1 0 26 67 1 0 26 68 1 0 27 69 1 0 27 70 1 0 29 71 1 0 29 72 1 0 29 73 1 0 34 74 1 0 34 75 1 0 34 76 1 0 37 77 1 0 37 78 1 0 37 79 1 0 40 80 1 0 40 81 1 0 40 82 1 0 43 83 1 6 44 84 1 0 44 85 1 0 46 86 1 0 46 87 1 0 46 88 1 0 47 89 1 0 47 90 1 0 48 91 1 0 48 92 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 NPC590468 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	35351
0.1-0.2	13889
0.2-0.3	374
0.3-0.4	111
0.4-0.5	41
0.5-0.6	41
0.6-0.7	25
0.7-0.8	2
0.8-0.85	7
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	NPC603853
0.8235	Intermediate Similarity	NPC76682
0.8235	Intermediate Similarity	NPC10908
0.8235	Intermediate Similarity	NPC63646
0.8235	Intermediate Similarity	NPC317145
0.8235	Intermediate Similarity	NPC198498
0.8235	Intermediate Similarity	NPC115284
0.8133	Intermediate Similarity	NPC212237
0.7857	Intermediate Similarity	NPC276890
0.7671	Intermediate Similarity	NPC73492
0.7671	Intermediate Similarity	NPC299990
0.7424	Intermediate Similarity	NPC247639
0.7424	Intermediate Similarity	NPC25084
0.7397	Intermediate Similarity	NPC12424
0.7397	Intermediate Similarity	NPC129518
0.7397	Intermediate Similarity	NPC251580
0.7368	Intermediate Similarity	NPC116465
0.726	Intermediate Similarity	NPC227060
0.7237	Intermediate Similarity	NPC311973
0.72	Intermediate Similarity	NPC290582
0.72	Intermediate Similarity	NPC217748
0.72	Intermediate Similarity	NPC182052
0.72	Intermediate Similarity	NPC271013
0.72	Intermediate Similarity	NPC42663
0.72	Intermediate Similarity	NPC15414
0.72	Intermediate Similarity	NPC480587
0.7105	Intermediate Similarity	NPC279228
0.6795	Remote Similarity	NPC239824
0.6709	Remote Similarity	NPC185639
0.6709	Remote Similarity	NPC251735
0.6709	Remote Similarity	NPC254441
0.6709	Remote Similarity	NPC49075
0.6709	Remote Similarity	NPC599951
0.65	Remote Similarity	NPC223690
0.65	Remote Similarity	NPC9532
0.642	Remote Similarity	NPC229373
0.6364	Remote Similarity	NPC603603
0.631	Remote Similarity	NPC24260
0.631	Remote Similarity	NPC611658
0.6265	Remote Similarity	NPC195538
0.6234	Remote Similarity	NPC41376
0.6232	Remote Similarity	NPC317439
0.619	Remote Similarity	NPC243454
0.6145	Remote Similarity	NPC181796
0.6145	Remote Similarity	NPC290005
0.6145	Remote Similarity	NPC54654
0.6145	Remote Similarity	NPC7715
0.6145	Remote Similarity	NPC328155
0.6145	Remote Similarity	NPC222661
0.6145	Remote Similarity	NPC285931
0.6	Remote Similarity	NPC475479
0.6	Remote Similarity	NPC323537
0.593	Remote Similarity	NPC485712
0.5909	Remote Similarity	NPC480590
0.5833	Remote Similarity	NPC274716
0.5833	Remote Similarity	NPC167116
0.5833	Remote Similarity	NPC609821
0.5795	Remote Similarity	NPC239584
0.5783	Remote Similarity	NPC475393
0.573	Remote Similarity	NPC480586
0.5714	Remote Similarity	NPC30779
0.5698	Remote Similarity	NPC16357
0.5698	Remote Similarity	NPC302245
0.5667	Remote Similarity	NPC281581
0.5618	Remote Similarity	NPC10871
0.5604	Remote Similarity	NPC485711
0.5595	Remote Similarity	NPC286119
0.5588	Remote Similarity	NPC213206
0.5588	Remote Similarity	NPC188163
0.5588	Remote Similarity	NPC328750
0.5584	Remote Similarity	NPC317272
0.5584	Remote Similarity	NPC268503
0.557	Remote Similarity	NPC256012
0.557	Remote Similarity	NPC610965
0.5517	Remote Similarity	NPC302275
0.5495	Remote Similarity	NPC82457
0.5441	Remote Similarity	NPC314682
0.5393	Remote Similarity	NPC8836
0.5393	Remote Similarity	NPC249996
0.5333	Remote Similarity	NPC104196
0.5326	Remote Similarity	NPC206900
0.5326	Remote Similarity	NPC11296
0.5326	Remote Similarity	NPC274661
0.5319	Remote Similarity	NPC41122
0.5319	Remote Similarity	NPC318805
0.5294	Remote Similarity	NPC608819
0.5238	Remote Similarity	NPC480591
0.5222	Remote Similarity	NPC275680
0.5222	Remote Similarity	NPC22115
0.5158	Remote Similarity	NPC475597
0.5122	Remote Similarity	NPC480592
0.5119	Remote Similarity	NPC240841
0.5057	Remote Similarity	NPC112248

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC590468 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5299
0.1-0.2	3743
0.2-0.3	94
0.3-0.4	8
0.4-0.5	2
0.5-0.6	1
0.6-0.7	0
0.7-0.8	2
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
0.8235	Intermediate Similarity	NPD8099	Discontinued
0.7778	Intermediate Similarity	NPD8156	Discontinued
0.7671	Intermediate Similarity	NPD8095	Phase 1
0.5588	Remote Similarity	NPD4664	Clinical (unspecified phase)

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