NPASS Compound

Natural Product: NPC607670

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 49 51 0 0 0 0 0 0 0 0999 V2000 5.9189 0.3904 -2.1113 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2649 0.9163 -1.0027 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1835 0.2561 -0.4310 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5629 0.8343 0.6878 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4733 0.2205 1.3042 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9901 -0.9748 0.8135 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8164 -1.6838 1.3837 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4393 -1.5394 0.6673 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1171 -0.2853 0.4623 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9085 0.9162 1.0622 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6504 2.0556 0.7209 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4163 3.2416 1.3325 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1809 4.3121 1.9082 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6362 1.9906 -0.2510 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3494 3.1228 -0.5664 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3528 3.0326 -1.5570 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8518 0.7774 -0.8572 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1293 -0.3455 -0.5306 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3466 -1.6932 -1.1181 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5321 -2.6062 0.0917 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4188 -2.5740 1.0128 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7584 -3.8819 0.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5924 -1.5538 -0.2862 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6606 -0.9270 -0.8699 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0849 -0.6998 -1.9304 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3582 0.5346 -3.0394 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9373 0.8311 -2.2427 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9222 1.7621 1.0847 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0198 0.6716 2.1807 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1213 -2.7635 1.3918 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8086 -1.4065 2.4607 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1700 -1.8808 -0.4240 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1830 1.0043 1.8377 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8060 4.2908 3.0004 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0373 5.0925 2.0230 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3656 4.9972 1.4292 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9553 3.9659 -1.5922 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0170 2.1465 -1.3808 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8964 2.8725 -2.5562 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6280 0.6820 -1.6369 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3356 -1.7295 -1.6409 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5730 -2.0324 -1.8032 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7547 -3.6300 -0.2234 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4209 -2.2057 0.6496 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5296 -4.6391 0.6191 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2984 -4.1262 1.8402 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0173 -3.8350 0.0924 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2120 -2.4949 -0.6728 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1141 -1.4093 -1.7344 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 3 1 0 21 8 1 0 18 9 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 5 29 1 0 7 30 1 0 7 31 1 0 8 32 1 0 10 33 1 0 13 34 1 0 13 35 1 0 13 36 1 0 16 37 1 0 16 38 1 0 16 39 1 0 17 40 1 0 19 41 1 0 19 42 1 0 20 43 1 0 20 44 1 0 22 45 1 0 22 46 1 0 22 47 1 0 23 48 1 0 24 49 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 NPC607670 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	31158
0.1-0.2	16727
0.2-0.3	1618
0.3-0.4	159
0.4-0.5	109
0.5-0.6	59
0.6-0.7	11
0.7-0.8	0
0.8-0.85	3
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	NPC314682
0.8444	Intermediate Similarity	NPC213206
0.8444	Intermediate Similarity	NPC188163
0.8444	Intermediate Similarity	NPC328750
0.7551	Intermediate Similarity	NPC185838
0.7451	Intermediate Similarity	NPC135538
0.7451	Intermediate Similarity	NPC24233
0.7358	Intermediate Similarity	NPC247639
0.7358	Intermediate Similarity	NPC25084
0.6949	Remote Similarity	NPC256012
0.6949	Remote Similarity	NPC610965
0.6724	Remote Similarity	NPC317272
0.6724	Remote Similarity	NPC268503
0.6119	Remote Similarity	NPC600054
0.6119	Remote Similarity	NPC601504
0.6111	Remote Similarity	NPC609731
0.6094	Remote Similarity	NPC603603
0.6	Remote Similarity	NPC240841
0.6	Remote Similarity	NPC147390
0.6	Remote Similarity	NPC428
0.5938	Remote Similarity	NPC276890
0.5926	Remote Similarity	NPC474915
0.5893	Remote Similarity	NPC317439
0.5862	Remote Similarity	NPC27887
0.5781	Remote Similarity	NPC76682
0.5781	Remote Similarity	NPC10908
0.5781	Remote Similarity	NPC63646
0.5781	Remote Similarity	NPC317145
0.5781	Remote Similarity	NPC198498
0.5781	Remote Similarity	NPC115284
0.5714	Remote Similarity	NPC191376
0.5652	Remote Similarity	NPC112248
0.5614	Remote Similarity	NPC321505
0.5614	Remote Similarity	NPC179825
0.5571	Remote Similarity	NPC601503
0.5522	Remote Similarity	NPC12424
0.5522	Remote Similarity	NPC129518
0.5522	Remote Similarity	NPC251580
0.5479	Remote Similarity	NPC601489
0.5479	Remote Similarity	NPC604804
0.5441	Remote Similarity	NPC603853
0.5429	Remote Similarity	NPC475393
0.5405	Remote Similarity	NPC605743
0.5373	Remote Similarity	NPC227060
0.5362	Remote Similarity	NPC290582
0.5362	Remote Similarity	NPC217748
0.5362	Remote Similarity	NPC73492
0.5362	Remote Similarity	NPC182052
0.5362	Remote Similarity	NPC271013
0.5362	Remote Similarity	NPC299990
0.5362	Remote Similarity	NPC42663
0.5362	Remote Similarity	NPC15414
0.5362	Remote Similarity	NPC480587
0.5342	Remote Similarity	NPC302275
0.5333	Remote Similarity	NPC475959
0.5286	Remote Similarity	NPC279228
0.5283	Remote Similarity	NPC128019
0.5263	Remote Similarity	NPC210437
0.5263	Remote Similarity	NPC16107
0.5263	Remote Similarity	NPC106295
0.5211	Remote Similarity	NPC311973
0.5211	Remote Similarity	NPC239824
0.5211	Remote Similarity	NPC600872
0.5172	Remote Similarity	NPC51957
0.5139	Remote Similarity	NPC185639
0.5139	Remote Similarity	NPC251735
0.5139	Remote Similarity	NPC116465
0.5139	Remote Similarity	NPC49075
0.5139	Remote Similarity	NPC223690
0.5139	Remote Similarity	NPC9532
0.5139	Remote Similarity	NPC599951
0.5102	Remote Similarity	NPC470926
0.5082	Remote Similarity	NPC104196
0.5077	Remote Similarity	NPC30779
0.5075	Remote Similarity	NPC480592
0.5072	Remote Similarity	NPC610959
0.5068	Remote Similarity	NPC274716
0.5068	Remote Similarity	NPC167116
0.5068	Remote Similarity	NPC609821

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607670 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4084
0.1-0.2	4642
0.2-0.3	380
0.3-0.4	33
0.4-0.5	5
0.5-0.6	5
0.6-0.7	0
0.7-0.8	0
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
0.8444	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.5781	Remote Similarity	NPD8099	Discontinued
0.5441	Remote Similarity	NPD8156	Discontinued
0.5362	Remote Similarity	NPD8095	Phase 1
0.5345	Remote Similarity	NPD4017	Phase 4
0.5263	Remote Similarity	NPD4584	Phase 2

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