NPASS Compound

Natural Product: NPC610129

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 53 0 0 0 0 0 0 0 0999 V2000 -6.7924 2.6895 -1.4302 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5541 2.3792 -1.4529 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6557 3.2626 -1.9895 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1547 1.0614 -0.8888 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7841 0.9555 -1.0271 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2500 -0.2254 -0.5331 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9153 0.0518 -0.2067 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7899 -0.5756 -0.6634 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7852 -1.6115 -1.5434 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3940 -2.1893 -1.9544 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4085 -3.2488 -2.8537 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5871 -1.7142 -1.4695 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7884 -2.2564 -1.8486 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8503 -3.2015 -2.6476 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9574 -1.7301 -1.3219 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8639 -0.6874 -0.4421 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0424 -0.0807 0.1535 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9040 0.9846 1.0499 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9784 1.5842 1.6323 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2490 1.1465 1.3460 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3567 1.7415 1.9267 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4144 0.1128 0.4783 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3079 -0.4967 -0.1147 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7022 -0.2002 -0.1071 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5828 -0.6651 -0.5782 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4132 -0.0875 -0.1669 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9068 -0.6407 0.7942 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0288 -1.4220 0.5495 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3846 0.6599 1.4075 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3661 1.5983 1.1930 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5866 1.0768 0.5688 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5835 0.1137 0.6989 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8163 4.2631 -1.9265 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6622 0.2923 -1.4804 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2865 -1.0523 -1.2371 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7095 -2.0118 -1.9463 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7931 -3.0943 -3.7765 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8850 -2.1556 -1.6204 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9104 1.3267 1.2736 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8118 2.4148 2.3272 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9944 1.1388 2.4232 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4028 -0.2436 0.2421 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4845 -1.3122 -0.7961 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4459 0.7348 0.5341 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1578 -1.1442 1.4261 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8672 -2.1582 -0.0768 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6111 0.5912 2.4680 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1779 2.1260 1.9906 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9529 2.0499 0.9014 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7497 -0.1507 1.6288 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 2 0 16 24 1 0 24 25 1 0 25 26 2 0 6 27 1 0 27 28 1 0 27 29 1 0 29 30 1 0 29 31 1 0 31 32 1 0 31 4 1 0 26 8 1 0 25 12 1 0 23 17 1 0 3 33 1 0 4 34 1 6 6 35 1 6 9 36 1 0 11 37 1 0 15 38 1 0 18 39 1 0 19 40 1 0 21 41 1 0 22 42 1 0 23 43 1 0 26 44 1 0 27 45 1 1 28 46 1 0 29 47 1 1 30 48 1 0 31 49 1 1 32 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 NPC610129 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	25624
0.1-0.2	21627
0.2-0.3	1786
0.3-0.4	593
0.4-0.5	152
0.5-0.6	47
0.6-0.7	18
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC282169
0.8889	High Similarity	NPC20505
0.8514	High Similarity	NPC608742
0.7792	Intermediate Similarity	NPC43211
0.7215	Intermediate Similarity	NPC210094
0.6795	Remote Similarity	NPC331652
0.679	Remote Similarity	NPC237435
0.6782	Remote Similarity	NPC64051
0.6709	Remote Similarity	NPC39360
0.6709	Remote Similarity	NPC29763
0.6709	Remote Similarity	NPC210003
0.6707	Remote Similarity	NPC610187
0.6522	Remote Similarity	NPC253685
0.6471	Remote Similarity	NPC600989
0.6463	Remote Similarity	NPC27942
0.6386	Remote Similarity	NPC135277
0.631	Remote Similarity	NPC115760
0.6265	Remote Similarity	NPC101191
0.6264	Remote Similarity	NPC229409
0.6098	Remote Similarity	NPC19709
0.6056	Remote Similarity	NPC234133
0.6024	Remote Similarity	NPC189142
0.6024	Remote Similarity	NPC77660
0.5889	Remote Similarity	NPC44931
0.587	Remote Similarity	NPC46202
0.5814	Remote Similarity	NPC235260
0.5814	Remote Similarity	NPC155763
0.5747	Remote Similarity	NPC601144
0.5684	Remote Similarity	NPC270675
0.5684	Remote Similarity	NPC195685
0.5647	Remote Similarity	NPC95090
0.5647	Remote Similarity	NPC27408
0.5618	Remote Similarity	NPC190003
0.5595	Remote Similarity	NPC473043
0.5581	Remote Similarity	NPC181712
0.5529	Remote Similarity	NPC261866
0.551	Remote Similarity	NPC472994
0.5506	Remote Similarity	NPC311830
0.5495	Remote Similarity	NPC606546
0.5484	Remote Similarity	NPC65003
0.5455	Remote Similarity	NPC49344
0.5408	Remote Similarity	NPC101636
0.5408	Remote Similarity	NPC298171
0.5385	Remote Similarity	NPC222674
0.5341	Remote Similarity	NPC138927
0.5333	Remote Similarity	NPC108406
0.5319	Remote Similarity	NPC210073
0.5294	Remote Similarity	NPC472993
0.5222	Remote Similarity	NPC22832
0.5222	Remote Similarity	NPC243930
0.5222	Remote Similarity	NPC264735
0.5172	Remote Similarity	NPC249281
0.5172	Remote Similarity	NPC108831
0.5172	Remote Similarity	NPC182634
0.5161	Remote Similarity	NPC8856
0.5155	Remote Similarity	NPC65711
0.5152	Remote Similarity	NPC479765
0.5114	Remote Similarity	NPC93337
0.5114	Remote Similarity	NPC297987
0.5114	Remote Similarity	NPC146792
0.5114	Remote Similarity	NPC323593
0.5114	Remote Similarity	NPC203500
0.5104	Remote Similarity	NPC122809
0.5102	Remote Similarity	NPC210961
0.5067	Remote Similarity	NPC127447
0.5067	Remote Similarity	NPC29353
0.5056	Remote Similarity	NPC105025
0.5056	Remote Similarity	NPC610763
0.5051	Remote Similarity	NPC479766
0.505	Remote Similarity	NPC179862

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610129 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4530
0.1-0.2	4529
0.2-0.3	81
0.3-0.4	8
0.4-0.5	1
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
0.679	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