NPASS Compound

Natural Product: NPC611247

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 48 49 0 0 0 0 0 0 0 0999 V2000 6.8352 0.0278 0.7817 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5735 -1.0047 -0.1237 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2664 -1.2726 -0.4929 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2224 -0.5326 0.0223 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9376 -0.8094 -0.3520 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8209 -0.0013 0.2132 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6154 1.1642 -0.7156 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5052 2.0310 -0.1986 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8562 2.4793 1.0655 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7978 1.2850 -0.2135 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8632 2.1800 0.2981 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6053 3.3111 0.6433 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2555 1.6960 0.3909 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3327 0.2815 -0.0868 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7322 -0.1864 0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5494 0.0040 -1.0729 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8506 -0.4276 -0.9881 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2923 -1.0285 0.1620 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4591 -1.2134 1.2465 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1505 -0.7815 1.1668 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6957 -1.8245 -1.2404 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7394 -2.5579 -1.7501 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0284 -2.3021 -1.3931 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1169 -3.0240 -1.8882 O 0 0 0 0 0 0 0 0 0 0 0 0 7.9322 0.2408 0.8244 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3201 0.9800 0.4669 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5406 -0.2605 1.8018 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4208 0.2707 0.7262 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9388 -0.6151 0.3940 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1659 0.3726 1.2142 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3919 0.7365 -1.7183 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5728 1.7322 -0.7435 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3850 2.9188 -0.8830 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2521 3.3831 1.0509 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0454 0.9457 -1.2550 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7872 0.3697 0.4074 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9382 2.3333 -0.2146 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5935 1.8023 1.4458 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7033 -0.3543 0.5905 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9323 0.1731 -1.0946 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1721 0.4797 -1.9626 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4961 -0.2865 -1.8228 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3138 -1.3653 0.2235 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8039 -1.6853 2.1514 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4808 -0.9114 1.9920 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6735 -2.0198 -1.5171 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5579 -3.3737 -2.4626 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7904 -3.3597 -1.2288 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 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 5 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 23 3 1 0 20 15 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 6 29 1 0 6 30 1 0 7 31 1 0 7 32 1 0 8 33 1 6 9 34 1 0 10 35 1 0 10 36 1 0 13 37 1 0 13 38 1 0 14 39 1 0 14 40 1 0 16 41 1 0 17 42 1 0 18 43 1 0 19 44 1 0 20 45 1 0 21 46 1 0 22 47 1 0 24 48 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 NPC611247 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	17361
0.1-0.2	26250
0.2-0.3	5545
0.3-0.4	548
0.4-0.5	88
0.5-0.6	26
0.6-0.7	20
0.7-0.8	0
0.8-0.85	0
0.85-0.9	4
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC275724
1.0	High Similarity	NPC244246
0.8958	High Similarity	NPC137427
0.8627	High Similarity	NPC215941
0.8627	High Similarity	NPC123196
0.8627	High Similarity	NPC311419
0.7963	Intermediate Similarity	NPC65935
0.7963	Intermediate Similarity	NPC319282
0.7959	Intermediate Similarity	NPC481914
0.7692	Intermediate Similarity	NPC481913
0.7451	Intermediate Similarity	NPC324571
0.7059	Intermediate Similarity	NPC321252
0.7059	Intermediate Similarity	NPC252544
0.6964	Remote Similarity	NPC20287
0.6964	Remote Similarity	NPC20404
0.6842	Remote Similarity	NPC12022
0.6842	Remote Similarity	NPC278308
0.6786	Remote Similarity	NPC229497
0.6667	Remote Similarity	NPC187725
0.6667	Remote Similarity	NPC141607
0.6667	Remote Similarity	NPC310194
0.6471	Remote Similarity	NPC312675
0.6471	Remote Similarity	NPC262156
0.6471	Remote Similarity	NPC127937
0.6471	Remote Similarity	NPC184651
0.6471	Remote Similarity	NPC113865
0.6316	Remote Similarity	NPC179777
0.6296	Remote Similarity	NPC473853
0.6296	Remote Similarity	NPC470212
0.6275	Remote Similarity	NPC177576
0.6078	Remote Similarity	NPC299406
0.6	Remote Similarity	NPC98631
0.6	Remote Similarity	NPC206615
0.5893	Remote Similarity	NPC53305
0.5789	Remote Similarity	NPC164386
0.5789	Remote Similarity	NPC343720
0.5789	Remote Similarity	NPC201777
0.5789	Remote Similarity	NPC54872
0.5789	Remote Similarity	NPC604524
0.5763	Remote Similarity	NPC257589
0.5741	Remote Similarity	NPC34634
0.5614	Remote Similarity	NPC265454
0.5593	Remote Similarity	NPC311595
0.5593	Remote Similarity	NPC24474
0.5593	Remote Similarity	NPC163083
0.5517	Remote Similarity	NPC303680
0.5439	Remote Similarity	NPC182240
0.5439	Remote Similarity	NPC5018
0.541	Remote Similarity	NPC310718
0.5345	Remote Similarity	NPC114298
0.5333	Remote Similarity	NPC123228
0.5333	Remote Similarity	NPC123722
0.5323	Remote Similarity	NPC304622
0.5312	Remote Similarity	NPC207613
0.5294	Remote Similarity	NPC8547
0.5254	Remote Similarity	NPC4181
0.5238	Remote Similarity	NPC84076
0.5082	Remote Similarity	NPC164778
0.5077	Remote Similarity	NPC90128

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611247 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3110
0.1-0.2	5493
0.2-0.3	533
0.3-0.4	13
0.4-0.5	1
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