NPASS Compound

Natural Product: NPC545095

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 36 39 0 0 0 0 0 0 0 0999 V2000 -5.2511 0.8507 0.5658 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2199 1.7350 0.3064 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9922 1.1890 -0.0043 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7853 -0.1765 -0.0583 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6666 -0.9492 -0.3447 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3516 -0.3571 -0.6723 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2776 0.1187 0.6373 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6125 0.7330 0.3724 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8976 2.1000 0.3838 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1983 2.3010 0.1069 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7756 1.0955 -0.0864 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0901 0.7298 -0.3986 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4006 -0.6060 -0.5415 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4199 -1.5700 -0.3773 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1236 -1.2227 -0.0702 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8138 0.1254 0.0735 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0420 -2.2891 -0.2534 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3461 -2.3219 0.0780 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.8177 -1.0651 0.2012 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0478 -0.5136 0.5128 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2082 1.2686 0.8073 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3889 2.8092 0.3494 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1797 1.8511 -0.2094 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2625 -1.1562 -1.1349 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4962 0.5106 -1.3473 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3625 0.8939 1.1006 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3322 -0.7126 1.3673 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1379 2.8318 0.5914 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7010 3.2316 0.0469 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7831 1.5348 -0.5075 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4345 -0.8464 -0.7847 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7150 -2.6071 -0.4996 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3658 -1.9969 0.0541 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3957 -3.1259 -0.4207 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9475 -3.1810 0.2287 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8427 -1.2125 0.7139 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 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 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 5 17 2 0 17 18 1 0 18 19 1 0 19 20 2 0 20 1 1 0 19 4 1 0 16 8 1 0 16 11 1 0 1 21 1 0 2 22 1 0 3 23 1 0 6 24 1 0 6 25 1 0 7 26 1 0 7 27 1 0 9 28 1 0 10 29 1 0 12 30 1 0 13 31 1 0 14 32 1 0 15 33 1 0 17 34 1 0 18 35 1 0 20 36 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 NPC545095 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	44302
0.1-0.2	4303
0.2-0.3	798
0.3-0.4	284
0.4-0.5	97
0.5-0.6	50
0.6-0.7	16
0.7-0.8	1
0.8-0.85	0
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	NPC601214
0.7429	Intermediate Similarity	NPC96102
0.7222	Intermediate Similarity	NPC230869
0.7222	Intermediate Similarity	NPC279081
0.7027	Intermediate Similarity	NPC29886
0.6842	Remote Similarity	NPC84911
0.6667	Remote Similarity	NPC73767
0.65	Remote Similarity	NPC310665
0.65	Remote Similarity	NPC605863
0.6389	Remote Similarity	NPC42372
0.619	Remote Similarity	NPC78020
0.6176	Remote Similarity	NPC261195
0.6136	Remote Similarity	NPC14113
0.6136	Remote Similarity	NPC145885
0.6136	Remote Similarity	NPC84827
0.6111	Remote Similarity	NPC216643
0.6111	Remote Similarity	NPC288838
0.6047	Remote Similarity	NPC315555
0.6047	Remote Similarity	NPC55772
0.6047	Remote Similarity	NPC59269
0.6047	Remote Similarity	NPC600736
0.5946	Remote Similarity	NPC105127
0.5946	Remote Similarity	NPC53947
0.5946	Remote Similarity	NPC102423
0.5946	Remote Similarity	NPC300149
0.5946	Remote Similarity	NPC230002
0.5909	Remote Similarity	NPC149155
0.5909	Remote Similarity	NPC203468
0.5909	Remote Similarity	NPC190296
0.5909	Remote Similarity	NPC110500
0.5909	Remote Similarity	NPC605329
0.5778	Remote Similarity	NPC480551
0.5778	Remote Similarity	NPC489200
0.5778	Remote Similarity	NPC480318
0.575	Remote Similarity	NPC604154
0.5652	Remote Similarity	NPC248041
0.5652	Remote Similarity	NPC489095
0.5652	Remote Similarity	NPC609424
0.5641	Remote Similarity	NPC131718
0.5532	Remote Similarity	NPC480317
0.5532	Remote Similarity	NPC200214
0.5532	Remote Similarity	NPC471957
0.5532	Remote Similarity	NPC469358
0.5532	Remote Similarity	NPC480316
0.5532	Remote Similarity	NPC608269
0.55	Remote Similarity	NPC138370
0.5417	Remote Similarity	NPC282231
0.5417	Remote Similarity	NPC267885
0.5417	Remote Similarity	NPC480550
0.5417	Remote Similarity	NPC480549
0.5366	Remote Similarity	NPC72435
0.5366	Remote Similarity	NPC601179
0.5306	Remote Similarity	NPC469780
0.5306	Remote Similarity	NPC469761
0.5306	Remote Similarity	NPC469783
0.5306	Remote Similarity	NPC469766
0.5306	Remote Similarity	NPC469779
0.5306	Remote Similarity	NPC469768
0.5306	Remote Similarity	NPC469784
0.5306	Remote Similarity	NPC489096
0.5306	Remote Similarity	NPC602670
0.5238	Remote Similarity	NPC154339
0.5238	Remote Similarity	NPC608908
0.52	Remote Similarity	NPC283219
0.52	Remote Similarity	NPC63751
0.52	Remote Similarity	NPC279918
0.5116	Remote Similarity	NPC111275
0.5098	Remote Similarity	NPC54988
0.5098	Remote Similarity	NPC480548
0.5098	Remote Similarity	NPC476460
0.5098	Remote Similarity	NPC609408

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC545095 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7659
0.1-0.2	1329
0.2-0.3	107
0.3-0.4	36
0.4-0.5	14
0.5-0.6	3
0.6-0.7	1
0.7-0.8	1
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
0.7429	Intermediate Similarity	NPD198	Clinical (unspecified phase)
0.65	Remote Similarity	NPD786	Pre-clinical
0.5909	Remote Similarity	NPD482	Phase 4
0.5778	Remote Similarity	NPD749	Clinical (unspecified phase)
0.5532	Remote Similarity	NPD1722	Phase 4

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