NPASS Compound

Natural Product: NPC606426

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 51 54 0 0 0 0 0 0 0 0999 V2000 5.8469 1.5333 -1.3002 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0005 1.8241 -0.0906 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1390 2.5312 0.2664 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9772 1.4079 0.8922 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9793 0.7245 0.2374 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1202 0.0697 1.1626 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0150 -0.3255 0.4006 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6889 0.0730 0.6008 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2873 0.9305 1.5995 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0262 1.3137 1.7834 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4060 2.1871 2.8072 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0001 0.8214 0.9313 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3062 1.2054 1.1179 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6515 1.9927 2.0402 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2487 0.6753 0.2249 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8205 -0.1797 -0.7643 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7494 -0.7667 -1.7265 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2639 -1.6246 -2.7037 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1056 -2.1901 -3.6192 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4491 -1.8984 -3.5621 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2857 -2.4980 -4.5197 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9299 -1.0523 -2.5988 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2901 -0.7703 -2.5582 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0859 -0.4691 -1.6603 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5396 -0.4976 -0.8726 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6178 -0.0391 -0.0757 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2954 -0.4179 -0.2519 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8560 -1.1099 1.7647 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5355 -1.1942 3.1177 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3338 -0.9037 1.5268 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5442 -1.0809 0.1508 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6762 0.5169 1.9238 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1638 0.7412 3.1980 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5938 3.1942 -0.3725 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6107 2.3428 1.3838 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9029 0.7573 1.9950 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0288 1.3294 2.2788 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8317 2.4290 3.5801 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2765 0.9564 0.3449 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2161 -1.8371 -2.7291 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7243 -2.8668 -4.3903 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1834 -2.0789 -4.6442 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5915 0.1306 -2.2136 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5209 0.1828 -0.9330 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0202 -1.0944 -1.0497 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5283 -2.0710 1.3164 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7559 -0.6251 3.3150 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9296 -1.6513 2.0973 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3752 -1.6182 0.0462 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7853 0.6851 1.8986 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7617 0.3051 3.8467 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 10 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 20 22 1 0 22 23 1 0 22 24 2 0 16 25 1 0 25 26 1 0 26 27 2 0 6 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 32 4 1 0 27 8 1 0 26 12 1 0 24 17 1 0 3 34 1 0 4 35 1 1 6 36 1 1 9 37 1 0 11 38 1 0 15 39 1 0 18 40 1 0 19 41 1 0 21 42 1 0 23 43 1 0 24 44 1 0 27 45 1 0 28 46 1 6 29 47 1 0 30 48 1 1 31 49 1 0 32 50 1 1 33 51 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 NPC606426 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	25971
0.1-0.2	21424
0.2-0.3	1676
0.3-0.4	573
0.4-0.5	149
0.5-0.6	37
0.6-0.7	19
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC20505
0.8889	High Similarity	NPC282169
0.8267	Intermediate Similarity	NPC608742
0.7273	Intermediate Similarity	NPC253685
0.7215	Intermediate Similarity	NPC135277
0.6923	Remote Similarity	NPC19709
0.6914	Remote Similarity	NPC43211
0.6835	Remote Similarity	NPC189142
0.6835	Remote Similarity	NPC77660
0.6818	Remote Similarity	NPC229409
0.6667	Remote Similarity	NPC600989
0.6585	Remote Similarity	NPC237435
0.6386	Remote Similarity	NPC210094
0.6353	Remote Similarity	NPC190003
0.631	Remote Similarity	NPC115760
0.6207	Remote Similarity	NPC606546
0.6197	Remote Similarity	NPC108406
0.619	Remote Similarity	NPC235260
0.619	Remote Similarity	NPC155763
0.6118	Remote Similarity	NPC610187
0.6071	Remote Similarity	NPC101191
0.6044	Remote Similarity	NPC64051
0.6	Remote Similarity	NPC49344
0.6	Remote Similarity	NPC210073
0.5976	Remote Similarity	NPC473043
0.5976	Remote Similarity	NPC331652
0.5904	Remote Similarity	NPC39360
0.5904	Remote Similarity	NPC29763
0.5904	Remote Similarity	NPC210003
0.5843	Remote Similarity	NPC8856
0.5806	Remote Similarity	NPC65711
0.5789	Remote Similarity	NPC605587
0.5747	Remote Similarity	NPC601144
0.5699	Remote Similarity	NPC46202
0.5698	Remote Similarity	NPC27942
0.5591	Remote Similarity	NPC115674
0.5568	Remote Similarity	NPC22832
0.5529	Remote Similarity	NPC261866
0.5517	Remote Similarity	NPC138927
0.5506	Remote Similarity	NPC311830
0.5495	Remote Similarity	NPC107987
0.5465	Remote Similarity	NPC95090
0.5465	Remote Similarity	NPC27408
0.5402	Remote Similarity	NPC181712
0.5349	Remote Similarity	NPC238376
0.5287	Remote Similarity	NPC277205
0.5287	Remote Similarity	NPC37919
0.5287	Remote Similarity	NPC136042
0.5227	Remote Similarity	NPC58716
0.5227	Remote Similarity	NPC84362
0.5227	Remote Similarity	NPC45638
0.5222	Remote Similarity	NPC243930
0.5213	Remote Similarity	NPC44931
0.52	Remote Similarity	NPC234133
0.52	Remote Similarity	NPC484301
0.5169	Remote Similarity	NPC201292
0.5114	Remote Similarity	NPC168822
0.5056	Remote Similarity	NPC271692
0.5055	Remote Similarity	NPC264735
0.5051	Remote Similarity	NPC270675
0.5051	Remote Similarity	NPC195685

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606426 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4550
0.1-0.2	4523
0.2-0.3	66
0.3-0.4	7
0.4-0.5	3
0.5-0.6	0
0.6-0.7	1
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
0.6585	Remote Similarity	NPD4338	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