NPASS Compound

Natural Product: NPC611369

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 68 73 0 0 0 0 0 0 0 0999 V2000 3.4431 -2.3391 -4.5033 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8022 -1.8924 -3.3629 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1389 -2.7814 -2.5266 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4899 -2.3690 -1.3817 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5185 -1.0343 -1.0873 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1811 -0.1410 -1.9216 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8259 -0.5344 -3.0549 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1304 1.2015 -1.4985 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2778 1.5515 -0.1191 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6249 2.1105 0.0190 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0456 3.0079 -0.9452 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3062 3.5734 -0.8766 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1369 3.2235 0.1750 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4066 3.7785 0.2645 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7043 2.3266 1.1306 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5318 1.9570 2.2071 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4507 1.7701 1.0542 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9718 0.3889 0.7798 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5423 0.7351 2.0346 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8765 -0.4069 0.1003 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1812 -1.3365 0.9802 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8351 -2.2454 1.7973 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2049 -2.2936 1.7983 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1506 -3.1142 2.6196 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2274 -3.1158 2.6642 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8853 -4.0073 3.5065 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8893 -2.2286 1.8672 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2080 -1.3679 1.0525 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9659 -0.5000 0.2756 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1917 -0.9276 -0.3316 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0495 0.2570 -0.5757 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7152 0.4679 -1.7613 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5044 1.5789 -1.9548 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1799 1.7925 -3.1585 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6523 2.5192 -0.9604 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4423 3.6571 -1.1168 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9851 2.3061 0.2251 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1185 3.2522 1.2604 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1930 1.1948 0.4245 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8566 -2.0239 0.4280 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2463 -1.8809 0.4213 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3687 -2.1688 1.8578 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0961 -3.1772 -4.9565 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1274 -3.8423 -2.7786 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9647 -3.0353 -0.7100 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3317 0.1918 -3.6808 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5384 2.3538 0.1403 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4170 3.3015 -1.7809 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6732 4.2779 -1.6080 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0289 3.5197 1.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4555 0.9819 2.5193 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1498 1.0616 1.8410 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9083 -0.2090 0.8719 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1809 1.6358 2.1313 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1463 0.3324 -0.2851 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7708 -2.4771 2.6231 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7033 -3.8159 3.2487 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0221 -3.7722 4.4837 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8941 -1.2974 -1.3542 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5978 -0.2792 -2.5526 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7313 2.4188 -3.8395 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3742 3.5824 -1.4966 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4259 3.3738 1.9778 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6853 1.0791 1.3942 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6059 -3.0070 -0.0674 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6760 -2.7785 0.3379 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8427 -3.0756 2.2713 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7349 -1.2849 2.4503 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 1 0 15 17 2 0 9 18 1 0 18 19 1 0 18 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 22 24 1 0 24 25 2 0 25 26 1 0 25 27 1 0 27 28 2 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 1 0 33 35 2 0 35 36 1 0 35 37 1 0 37 38 1 0 37 39 2 0 30 40 1 0 40 41 1 0 40 42 1 0 7 2 1 0 17 10 1 0 28 21 1 0 39 31 1 0 20 5 1 0 42 27 1 0 1 43 1 0 3 44 1 0 4 45 1 0 7 46 1 0 9 47 1 1 11 48 1 0 12 49 1 0 14 50 1 0 16 51 1 0 17 52 1 0 18 53 1 1 19 54 1 0 20 55 1 6 23 56 1 0 24 57 1 0 26 58 1 0 30 59 1 6 32 60 1 0 34 61 1 0 36 62 1 0 38 63 1 0 39 64 1 0 40 65 1 6 41 66 1 0 42 67 1 0 42 68 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 NPC611369 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	22326
0.1-0.2	24583
0.2-0.3	2624
0.3-0.4	187
0.4-0.5	53
0.5-0.6	38
0.6-0.7	16
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	11
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC600630
1.0	High Similarity	NPC607896
0.9355	High Similarity	NPC313116
0.9355	High Similarity	NPC603340
0.9219	High Similarity	NPC601997
0.9219	High Similarity	NPC609211
0.9219	High Similarity	NPC610665
0.9062	High Similarity	NPC70409
0.9062	High Similarity	NPC204770
0.9062	High Similarity	NPC600551
0.9062	High Similarity	NPC601980
0.9062	High Similarity	NPC602065
0.9062	High Similarity	NPC611024
0.8281	Intermediate Similarity	NPC601999
0.7727	Intermediate Similarity	NPC58190
0.7727	Intermediate Similarity	NPC108811
0.7727	Intermediate Similarity	NPC170103
0.7727	Intermediate Similarity	NPC236202
0.7727	Intermediate Similarity	NPC262911
0.7727	Intermediate Similarity	NPC202742
0.7612	Intermediate Similarity	NPC246202
0.7612	Intermediate Similarity	NPC224161
0.7612	Intermediate Similarity	NPC46335
0.7612	Intermediate Similarity	NPC279406
0.7612	Intermediate Similarity	NPC486519
0.7424	Intermediate Similarity	NPC96576
0.7123	Intermediate Similarity	NPC278548
0.6714	Remote Similarity	NPC82917
0.64	Remote Similarity	NPC226809
0.64	Remote Similarity	NPC211561
0.6329	Remote Similarity	NPC135021
0.6164	Remote Similarity	NPC294558
0.6164	Remote Similarity	NPC18185
0.6164	Remote Similarity	NPC263940
0.6145	Remote Similarity	NPC86630
0.6098	Remote Similarity	NPC147743
0.6098	Remote Similarity	NPC4809
0.6098	Remote Similarity	NPC73517
0.6071	Remote Similarity	NPC106601
0.6071	Remote Similarity	NPC151474
0.6026	Remote Similarity	NPC302549
0.6	Remote Similarity	NPC212614
0.6	Remote Similarity	NPC205613
0.5904	Remote Similarity	NPC9309
0.5867	Remote Similarity	NPC184245
0.5867	Remote Similarity	NPC187801
0.5867	Remote Similarity	NPC610920
0.5802	Remote Similarity	NPC306267
0.5797	Remote Similarity	NPC178054
0.5795	Remote Similarity	NPC159526
0.5758	Remote Similarity	NPC261619
0.5758	Remote Similarity	NPC61477
0.5758	Remote Similarity	NPC78770
0.5758	Remote Similarity	NPC219876
0.5758	Remote Similarity	NPC126029
0.5758	Remote Similarity	NPC15658
0.575	Remote Similarity	NPC44192
0.5679	Remote Similarity	NPC20050
0.56	Remote Similarity	NPC277331
0.56	Remote Similarity	NPC100482
0.5517	Remote Similarity	NPC78074
0.5495	Remote Similarity	NPC478617
0.5455	Remote Similarity	NPC268266
0.5455	Remote Similarity	NPC42760
0.5455	Remote Similarity	NPC220825
0.5455	Remote Similarity	NPC268342
0.5432	Remote Similarity	NPC46283
0.5432	Remote Similarity	NPC65333
0.5432	Remote Similarity	NPC469944
0.5341	Remote Similarity	NPC478340
0.5309	Remote Similarity	NPC272552
0.5309	Remote Similarity	NPC226108
0.5309	Remote Similarity	NPC322899
0.5303	Remote Similarity	NPC601844
0.5281	Remote Similarity	NPC478337
0.5281	Remote Similarity	NPC478338
0.5256	Remote Similarity	NPC165483
0.5238	Remote Similarity	NPC478616
0.5238	Remote Similarity	NPC478339
0.5111	Remote Similarity	NPC479793
0.506	Remote Similarity	NPC134911

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611369 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4872
0.1-0.2	4234
0.2-0.3	34
0.3-0.4	8
0.4-0.5	0
0.5-0.6	2
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
0.5758	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.5758	Remote Similarity	NPD1613	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