NPASS Compound

Natural Product: NPC611064

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 67 69 0 0 0 0 0 0 0 0999 V2000 0.4524 -3.1734 3.7798 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1309 -2.1910 3.1866 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4010 -0.9926 2.7787 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4229 -0.6720 1.3176 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3854 0.5786 1.1215 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9189 0.8122 -0.2494 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8559 1.9765 -0.1996 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0211 1.8510 0.6840 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2345 2.0447 0.2349 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4082 1.9133 1.1338 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4594 2.4232 -1.1737 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4613 -0.3667 -0.9725 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7257 0.0449 -2.4145 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7463 -0.8858 -0.3975 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4323 -1.4772 -0.9206 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7874 -2.7047 -1.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3623 -3.6760 -1.5241 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0373 -4.0942 -2.5686 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8683 -0.9444 -1.4489 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1105 -1.0661 -2.6601 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8566 -0.2823 -0.5596 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8509 0.5633 -1.1473 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8571 0.5652 -2.4583 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8381 1.4079 -0.5345 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8513 1.7820 0.7651 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8911 2.5499 1.3164 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9353 2.9494 0.5413 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9515 2.5910 -0.7753 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9304 1.8389 -1.3046 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7953 -0.6059 0.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9434 -0.8499 1.4359 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2390 -1.7840 0.5191 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5680 -2.8219 1.0484 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6149 -3.1159 3.9694 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9404 -4.0853 4.1039 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1925 -2.3358 3.0405 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6763 -1.0801 3.0604 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7459 -0.0683 3.3058 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3048 1.4352 1.3533 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2147 0.5282 1.8631 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0270 1.1582 -0.8695 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 2.8880 0.1513 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1990 2.2997 -1.2102 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9088 1.5977 1.7314 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7424 2.9536 1.3709 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2698 1.4251 0.5953 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1946 1.3447 2.0516 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9074 3.3896 -1.3455 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0237 1.6833 -1.8691 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5473 2.5574 -1.3693 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5096 1.1024 -2.5936 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1128 -0.5269 -3.1460 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7760 -0.1689 -2.6948 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8197 -1.9774 -0.3691 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9027 -0.5460 0.6523 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5949 -0.4849 -0.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7199 -3.1757 -1.4048 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7740 -2.4385 -2.7893 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6406 -4.0345 -0.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7695 -3.7437 -3.5544 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8545 -4.7850 -2.4331 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0573 1.5666 1.4344 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8859 2.8384 2.3593 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7327 3.5460 0.9920 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7999 2.9273 -1.3675 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0066 1.5907 -2.3535 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6219 -1.5689 1.2763 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 4 3 1 1 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 3 9 10 1 0 9 11 1 0 6 12 1 0 12 13 1 0 12 14 1 0 12 15 1 0 15 16 1 6 16 17 1 0 17 18 2 0 15 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 21 30 2 0 30 31 1 0 15 32 1 0 32 33 2 0 30 4 1 0 32 4 1 0 29 24 1 0 1 34 1 0 1 35 1 0 2 36 1 0 3 37 1 0 3 38 1 0 5 39 1 0 5 40 1 0 6 41 1 6 7 42 1 0 7 43 1 0 8 44 1 0 10 45 1 0 10 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 11 50 1 0 13 51 1 0 13 52 1 0 13 53 1 0 14 54 1 0 14 55 1 0 14 56 1 0 16 57 1 0 16 58 1 0 17 59 1 0 18 60 1 0 18 61 1 0 25 62 1 0 26 63 1 0 27 64 1 0 28 65 1 0 29 66 1 0 31 67 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 NPC611064 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	8039
0.1-0.2	39805
0.2-0.3	1852
0.3-0.4	87
0.4-0.5	28
0.5-0.6	21
0.6-0.7	22
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8929	High Similarity	NPC259400
0.8929	High Similarity	NPC130591
0.8929	High Similarity	NPC234637
0.7385	Intermediate Similarity	NPC600618
0.6923	Remote Similarity	NPC149773
0.6438	Remote Similarity	NPC603871
0.6429	Remote Similarity	NPC46242
0.6429	Remote Similarity	NPC479147
0.6429	Remote Similarity	NPC91887
0.6429	Remote Similarity	NPC93556
0.6338	Remote Similarity	NPC297797
0.6308	Remote Similarity	NPC471481
0.6308	Remote Similarity	NPC610194
0.6271	Remote Similarity	NPC605738
0.625	Remote Similarity	NPC51531
0.6164	Remote Similarity	NPC165191
0.6164	Remote Similarity	NPC469857
0.6164	Remote Similarity	NPC30846
0.6164	Remote Similarity	NPC245760
0.6164	Remote Similarity	NPC177501
0.6133	Remote Similarity	NPC237441
0.6027	Remote Similarity	NPC114333
0.6027	Remote Similarity	NPC28592
0.6	Remote Similarity	NPC471971
0.6	Remote Similarity	NPC471972
0.6	Remote Similarity	NPC469855
0.5946	Remote Similarity	NPC473479
0.5946	Remote Similarity	NPC50615
0.5946	Remote Similarity	NPC141650
0.589	Remote Similarity	NPC198803
0.5658	Remote Similarity	NPC294330
0.5634	Remote Similarity	NPC608846
0.5616	Remote Similarity	NPC289358
0.5616	Remote Similarity	NPC4289
0.5616	Remote Similarity	NPC42384
0.5584	Remote Similarity	NPC469854
0.5571	Remote Similarity	NPC218855
0.5513	Remote Similarity	NPC469856
0.5443	Remote Similarity	NPC471970
0.541	Remote Similarity	NPC602123
0.5316	Remote Similarity	NPC25736
0.5238	Remote Similarity	NPC600619
0.519	Remote Similarity	NPC5014
0.5067	Remote Similarity	NPC483069
0.5063	Remote Similarity	NPC23667
0.5063	Remote Similarity	NPC157284
0.5063	Remote Similarity	NPC479151

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2701
0.1-0.2	6308
0.2-0.3	140
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
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
		NPD

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