NPASS Compound

Natural Product: NPC552071

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 54 0 0 0 0 0 0 0 0999 V2000 -4.6132 3.7955 0.8976 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4718 2.4438 0.5609 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2484 1.8514 0.2601 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2505 2.6330 0.3125 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1189 0.4540 -0.0858 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2343 -0.2766 -0.1103 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1880 -1.6315 -0.4352 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0062 -2.3693 -0.5159 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1191 -3.7804 -0.0359 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9141 -1.5917 0.2323 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6649 -2.3787 0.1534 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5478 -1.6562 0.1838 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3438 -1.7869 1.3469 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8206 -1.5937 0.9782 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9169 -0.2569 0.3441 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8323 0.2908 -0.3273 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2394 1.4916 -0.7794 N 0 0 0 0 0 0 0 0 0 0 0 0 3.5231 1.7125 -0.4198 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3741 2.7840 -0.6445 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6558 2.7476 -0.1568 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1337 1.6658 0.5598 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2654 0.6105 0.7701 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9719 0.6228 0.2902 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5506 -0.3953 -0.4533 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6214 0.4920 -0.0108 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8638 -0.2294 -0.4124 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1943 4.2869 0.0791 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6254 4.2677 0.9031 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1439 3.9411 1.8802 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2043 0.1430 0.1166 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6498 -2.3793 -1.5876 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6894 -3.8913 0.9864 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1975 -4.0356 0.0460 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6175 -4.4725 -0.7488 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2353 -1.4508 1.2872 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6594 -3.0992 1.0236 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6841 -2.9936 -0.7844 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2697 -2.8318 1.7133 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0636 -1.1300 2.1892 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0180 -2.3653 0.1810 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4780 -1.6988 1.8449 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6953 2.1994 -1.3330 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0211 3.6572 -1.2110 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3361 3.5914 -0.3302 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1417 1.6619 0.9309 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6011 -0.2571 1.3274 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3669 -0.5676 -1.5539 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5821 0.7294 1.0508 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5254 1.4088 -0.6631 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8441 -0.3626 -1.5252 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 16 24 1 0 24 25 1 0 25 26 1 0 26 5 1 0 26 10 1 0 24 12 1 0 23 15 1 0 23 18 1 0 1 27 1 0 1 28 1 0 1 29 1 0 6 30 1 0 8 31 1 6 9 32 1 0 9 33 1 0 9 34 1 0 10 35 1 1 11 36 1 0 11 37 1 0 13 38 1 0 13 39 1 0 14 40 1 0 14 41 1 0 17 42 1 0 19 43 1 0 20 44 1 0 21 45 1 0 22 46 1 0 24 47 1 6 25 48 1 0 25 49 1 0 26 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 NPC552071 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	21351
0.1-0.2	27412
0.2-0.3	838
0.3-0.4	175
0.4-0.5	37
0.5-0.6	26
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC312870
1.0	High Similarity	NPC199851
1.0	High Similarity	NPC294909
1.0	High Similarity	NPC254240
1.0	High Similarity	NPC128265
1.0	High Similarity	NPC604675
0.7949	Intermediate Similarity	NPC603895
0.7848	Intermediate Similarity	NPC21638
0.7763	Intermediate Similarity	NPC486449
0.7763	Intermediate Similarity	NPC63199
0.7763	Intermediate Similarity	NPC111602
0.7763	Intermediate Similarity	NPC102338
0.7763	Intermediate Similarity	NPC196251
0.7532	Intermediate Similarity	NPC273374
0.6585	Remote Similarity	NPC107782
0.6585	Remote Similarity	NPC486454
0.6071	Remote Similarity	NPC486443
0.6071	Remote Similarity	NPC486446
0.6	Remote Similarity	NPC175474
0.6	Remote Similarity	NPC99921
0.5952	Remote Similarity	NPC486452
0.5952	Remote Similarity	NPC74591
0.593	Remote Similarity	NPC100898
0.593	Remote Similarity	NPC148183
0.593	Remote Similarity	NPC21084
0.593	Remote Similarity	NPC152768
0.593	Remote Similarity	NPC605270
0.5833	Remote Similarity	NPC220151
0.5833	Remote Similarity	NPC19692
0.5795	Remote Similarity	NPC293861
0.5747	Remote Similarity	NPC131260
0.57	Remote Similarity	NPC486444
0.57	Remote Similarity	NPC649
0.5698	Remote Similarity	NPC313985
0.5698	Remote Similarity	NPC249150
0.5698	Remote Similarity	NPC33619
0.5632	Remote Similarity	NPC81654
0.5625	Remote Similarity	NPC21174
0.5422	Remote Similarity	NPC474897
0.5366	Remote Similarity	NPC185200
0.5366	Remote Similarity	NPC229173
0.52	Remote Similarity	NPC191489
0.5192	Remote Similarity	NPC199607
0.5192	Remote Similarity	NPC54591
0.5169	Remote Similarity	NPC483467
0.5059	Remote Similarity	NPC165441

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC552071 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3778
0.1-0.2	5211
0.2-0.3	142
0.3-0.4	10
0.4-0.5	4
0.5-0.6	3
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	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4500	Approved
1.0	High Similarity	NPD4501	Approved
0.5698	Remote Similarity	NPD4601	Phase 4
0.5632	Remote Similarity	NPD4600	Approved
0.52	Remote Similarity	NPD7708	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