NPASS Compound

Natural Product: NPC606439

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 50 52 0 0 0 0 0 0 0 0999 V2000 6.6518 0.1029 2.4005 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5251 0.7988 2.8952 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2462 0.4502 2.4374 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0948 -0.5491 1.5255 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8393 -0.9022 1.0663 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6879 -0.2645 1.5061 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3294 -0.6304 1.0262 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0943 0.1456 -0.1926 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4560 -0.2766 -0.5996 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0788 -1.3763 -0.0179 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3395 -1.6912 -0.4707 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9760 -2.7866 0.0993 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3537 -3.5540 1.1098 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9928 -0.9724 -1.4575 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2608 -1.3097 -1.8956 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8558 -0.5234 -2.9066 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3235 0.1180 -2.0043 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0632 0.4728 -1.5855 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2886 1.6272 -2.1123 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8620 2.3630 -0.8286 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0845 1.5487 -0.1005 N 0 0 0 0 0 0 0 0 0 0 0 0 1.4086 1.9636 -0.5860 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8583 0.7464 2.4305 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1186 1.1011 2.8918 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2837 2.1339 3.8352 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5501 0.4056 2.9603 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5500 -1.0017 2.5235 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8231 0.3410 1.3174 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9892 -1.0651 1.1654 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7673 -1.6928 0.3503 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4158 -1.7038 0.6726 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4417 -0.5154 1.8032 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5752 -0.2015 -1.0382 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5852 -1.9644 0.7681 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9560 -4.4069 1.4183 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3175 -3.8678 0.7948 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1960 -2.8608 1.9716 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2737 -0.6215 -3.8572 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8994 -0.8084 -3.1072 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8631 0.5562 -2.6478 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7929 0.7074 -2.7754 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4134 1.3296 -2.6884 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9682 2.3169 -2.6712 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8081 2.4568 -0.2345 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4186 3.3358 -1.0647 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8664 2.5929 0.2015 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9964 1.0802 -0.8634 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3453 2.6080 -1.4855 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0296 1.3089 2.8398 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8424 2.9350 3.5057 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 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 11 14 2 0 14 15 1 0 15 16 1 0 14 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 6 23 1 0 23 24 2 0 24 25 1 0 24 3 1 0 21 8 1 0 18 9 1 0 1 26 1 0 1 27 1 0 1 28 1 0 4 29 1 0 5 30 1 0 7 31 1 0 7 32 1 0 8 33 1 0 10 34 1 0 13 35 1 0 13 36 1 0 13 37 1 0 16 38 1 0 16 39 1 0 16 40 1 0 17 41 1 0 19 42 1 0 19 43 1 0 20 44 1 0 20 45 1 0 22 46 1 0 22 47 1 0 22 48 1 0 23 49 1 0 25 50 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 NPC606439 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	26679
0.1-0.2	20002
0.2-0.3	2710
0.3-0.4	247
0.4-0.5	137
0.5-0.6	52
0.6-0.7	13
0.7-0.8	1
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC135538
1.0	High Similarity	NPC24233
0.8269	Intermediate Similarity	NPC147390
0.8269	Intermediate Similarity	NPC428
0.7451	Intermediate Similarity	NPC314682
0.7308	Intermediate Similarity	NPC213206
0.7308	Intermediate Similarity	NPC188163
0.7308	Intermediate Similarity	NPC328750
0.7222	Intermediate Similarity	NPC185838
0.6923	Remote Similarity	NPC603603
0.6912	Remote Similarity	NPC600872
0.6818	Remote Similarity	NPC240841
0.6774	Remote Similarity	NPC317272
0.6774	Remote Similarity	NPC268503
0.6667	Remote Similarity	NPC191376
0.6552	Remote Similarity	NPC321505
0.6552	Remote Similarity	NPC179825
0.6462	Remote Similarity	NPC256012
0.6462	Remote Similarity	NPC610965
0.623	Remote Similarity	NPC247639
0.623	Remote Similarity	NPC25084
0.6119	Remote Similarity	NPC480592
0.5932	Remote Similarity	NPC609731
0.5857	Remote Similarity	NPC610959
0.5789	Remote Similarity	NPC601489
0.5789	Remote Similarity	NPC604804
0.5753	Remote Similarity	NPC311973
0.5753	Remote Similarity	NPC286119
0.5753	Remote Similarity	NPC239824
0.5753	Remote Similarity	NPC600054
0.5753	Remote Similarity	NPC601504
0.5479	Remote Similarity	NPC290582
0.5479	Remote Similarity	NPC217748
0.5479	Remote Similarity	NPC182052
0.5479	Remote Similarity	NPC271013
0.5479	Remote Similarity	NPC42663
0.5479	Remote Similarity	NPC15414
0.5467	Remote Similarity	NPC254441
0.5467	Remote Similarity	NPC601503
0.5439	Remote Similarity	NPC34559
0.5405	Remote Similarity	NPC279228
0.5325	Remote Similarity	NPC181796
0.5325	Remote Similarity	NPC290005
0.5325	Remote Similarity	NPC54654
0.5325	Remote Similarity	NPC7715
0.5325	Remote Similarity	NPC328155
0.5325	Remote Similarity	NPC222661
0.5325	Remote Similarity	NPC285931
0.5323	Remote Similarity	NPC103379
0.5312	Remote Similarity	NPC276588
0.5312	Remote Similarity	NPC127674
0.5312	Remote Similarity	NPC278799
0.5263	Remote Similarity	NPC185639
0.5263	Remote Similarity	NPC251735
0.5263	Remote Similarity	NPC49075
0.5263	Remote Similarity	NPC223690
0.5263	Remote Similarity	NPC9532
0.5263	Remote Similarity	NPC599951
0.5246	Remote Similarity	NPC474915
0.5238	Remote Similarity	NPC151895
0.5231	Remote Similarity	NPC104196
0.5231	Remote Similarity	NPC27887
0.5195	Remote Similarity	NPC274716
0.5195	Remote Similarity	NPC167116
0.5195	Remote Similarity	NPC609821
0.519	Remote Similarity	NPC212237
0.5156	Remote Similarity	NPC39701
0.5156	Remote Similarity	NPC184026
0.5152	Remote Similarity	NPC253043
0.5152	Remote Similarity	NPC136508
0.5152	Remote Similarity	NPC600388
0.5139	Remote Similarity	NPC276890
0.5125	Remote Similarity	NPC605743
0.5065	Remote Similarity	NPC116465

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606439 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3877
0.1-0.2	4971
0.2-0.3	265
0.3-0.4	26
0.4-0.5	8
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7308	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.5873	Remote Similarity	NPD4010	Discontinued

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