NPASS Compound

Natural Product: NPC611318

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 51 0 0 0 0 0 0 0 0999 V2000 0.3628 -3.2855 -0.1202 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2906 -2.4423 0.6266 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5858 -2.5753 2.0260 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0604 -3.4329 2.8179 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5390 -1.6241 2.4011 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3888 -0.5623 1.5397 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6803 0.1264 1.2221 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8187 1.4261 1.1030 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8052 2.4680 1.2737 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1619 1.8642 0.4815 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6337 2.3815 -0.9620 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5066 1.3617 -1.1378 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2930 1.6074 -1.5400 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0062 3.1065 -1.9182 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0604 0.8287 -1.3825 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1218 -0.2813 -0.4595 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3593 -0.9884 -0.7150 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5048 -0.8969 -0.0074 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5431 -0.1304 0.9823 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6736 -1.6958 -0.4147 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5895 -2.5926 -1.5927 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8165 -1.6430 0.2425 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9449 -0.7688 1.4149 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8774 -1.1399 0.1683 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5579 -3.1293 -1.1861 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7679 -4.2198 0.2671 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6455 0.1740 1.8524 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5275 -0.5836 1.1047 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7600 2.1525 1.1997 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0477 3.4098 0.7282 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8987 2.7945 2.3712 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5851 2.7175 0.9347 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7658 1.0065 0.3170 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3218 3.3813 -0.8315 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4517 2.1908 -1.6122 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8847 0.3408 -0.9620 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3142 3.0196 -2.7768 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9221 3.5586 -2.2668 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4898 3.5383 -1.0715 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7953 1.5817 -1.2335 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1477 0.4363 -2.4681 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5285 0.3193 0.5105 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7134 -2.2754 -2.1933 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3383 -3.6070 -1.1975 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5273 -2.6019 -2.1816 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6672 -2.2455 -0.0806 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9924 -0.8348 1.8328 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8385 0.2861 1.0946 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2801 -1.0659 2.2329 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7482 -1.4558 -0.4337 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 20 22 2 0 22 23 1 0 16 24 1 0 24 2 1 0 24 6 1 0 1 25 1 0 1 26 1 0 6 27 1 1 7 28 1 0 9 29 1 0 9 30 1 0 9 31 1 0 10 32 1 0 10 33 1 0 11 34 1 0 11 35 1 0 12 36 1 0 14 37 1 0 14 38 1 0 14 39 1 0 15 40 1 0 15 41 1 0 16 42 1 1 21 43 1 0 21 44 1 0 21 45 1 0 22 46 1 0 23 47 1 0 23 48 1 0 23 49 1 0 24 50 1 6 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 NPC611318 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	23126
0.1-0.2	23555
0.2-0.3	2512
0.3-0.4	442
0.4-0.5	148
0.5-0.6	46
0.6-0.7	15
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.878	High Similarity	NPC171204
0.878	High Similarity	NPC606745
0.7551	Intermediate Similarity	NPC470755
0.7551	Intermediate Similarity	NPC298801
0.7021	Intermediate Similarity	NPC270126
0.68	Remote Similarity	NPC481909
0.68	Remote Similarity	NPC158756
0.68	Remote Similarity	NPC601035
0.6415	Remote Similarity	NPC469910
0.64	Remote Similarity	NPC250940
0.64	Remote Similarity	NPC169575
0.6327	Remote Similarity	NPC609300
0.617	Remote Similarity	NPC97516
0.6087	Remote Similarity	NPC58956
0.6087	Remote Similarity	NPC163003
0.6087	Remote Similarity	NPC295633
0.6087	Remote Similarity	NPC269206
0.6071	Remote Similarity	NPC481911
0.6038	Remote Similarity	NPC482131
0.6	Remote Similarity	NPC476028
0.5918	Remote Similarity	NPC488306
0.5849	Remote Similarity	NPC178702
0.5686	Remote Similarity	NPC610417
0.5556	Remote Similarity	NPC473619
0.5536	Remote Similarity	NPC481806
0.5536	Remote Similarity	NPC269509
0.551	Remote Similarity	NPC167881
0.551	Remote Similarity	NPC98557
0.5472	Remote Similarity	NPC488302
0.5472	Remote Similarity	NPC475461
0.5472	Remote Similarity	NPC488300
0.5472	Remote Similarity	NPC116177
0.5472	Remote Similarity	NPC488301
0.5472	Remote Similarity	NPC165383
0.5455	Remote Similarity	NPC320630
0.5439	Remote Similarity	NPC40746
0.537	Remote Similarity	NPC473390
0.537	Remote Similarity	NPC488296
0.5357	Remote Similarity	NPC482130
0.5357	Remote Similarity	NPC482128
0.5357	Remote Similarity	NPC482129
0.5357	Remote Similarity	NPC605339
0.5283	Remote Similarity	NPC470256
0.5283	Remote Similarity	NPC50637
0.5283	Remote Similarity	NPC476355
0.5283	Remote Similarity	NPC600792
0.5283	Remote Similarity	NPC610427
0.5273	Remote Similarity	NPC488298
0.5273	Remote Similarity	NPC272814
0.5273	Remote Similarity	NPC488297
0.5185	Remote Similarity	NPC7563
0.5185	Remote Similarity	NPC609663
0.5179	Remote Similarity	NPC281132
0.5179	Remote Similarity	NPC482126
0.5179	Remote Similarity	NPC202672
0.5179	Remote Similarity	NPC266957
0.5179	Remote Similarity	NPC250315
0.5172	Remote Similarity	NPC486031
0.5091	Remote Similarity	NPC194871
0.5091	Remote Similarity	NPC607063
0.5091	Remote Similarity	NPC607495
0.5091	Remote Similarity	NPC610688
0.5088	Remote Similarity	NPC307411
0.5085	Remote Similarity	NPC134725
0.5085	Remote Similarity	NPC48657
0.5082	Remote Similarity	NPC482132

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611318 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7313
0.1-0.2	1798
0.2-0.3	35
0.3-0.4	4
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