NPASS Compound

Natural Product: NPC611827

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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0 0 0 0 0 0 0 0 0 -18.1631 5.8477 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -16.8010 3.2312 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -14.6490 2.5352 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -16.5448 3.1329 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -13.8246 4.3440 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 5 7 1 0 5 8 1 0 8 9 2 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 15 17 1 0 17 18 1 0 18 19 1 0 18 20 1 0 18 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 24 25 1 0 24 26 1 0 26 27 2 0 26 28 1 0 28 29 1 0 29 30 1 0 29 31 1 0 29 32 1 0 32 33 2 0 32 34 1 0 34 35 1 0 35 36 1 0 35 37 1 0 37 38 2 0 37 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 43 45 2 0 40 46 1 0 46 47 2 0 46 48 1 0 48 49 1 0 49 50 1 0 49 51 1 0 49 52 1 0 52 53 2 0 52 54 1 0 54 55 1 0 55 56 1 0 56 57 2 0 56 58 1 0 58 59 1 0 59 60 1 0 59 61 1 0 59 62 1 0 62 63 2 0 62 64 1 0 64 65 1 0 65 66 1 0 66 67 2 0 66 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 71 72 1 0 71 73 1 0 69 74 1 0 74 75 2 0 74 76 1 0 76 77 1 0 77 78 1 0 77 79 1 0 77 80 1 0 80 81 2 0 80 82 1 0 82 83 1 0 83 84 1 0 84 85 1 0 85 86 1 0 86 87 1 0 87 88 2 0 87 89 1 0 89 90 1 0 90 91 1 0 91 92 2 0 91 93 1 0 93 94 1 0 94 95 1 0 94 96 1 0 94 97 1 0 97 98 2 0 97 99 1 0 99100 1 0 100101 1 0 100102 1 0 100103 1 0 103104 2 0 103105 1 0 105106 1 0 106107 1 0 107108 1 0 108109 1 0 109110 1 0 109111 2 0 106112 1 0 112113 2 0 112114 1 0 114115 1 0 115116 1 0 116117 1 0 117118 1 0 118119 1 0 118120 2 0 115121 1 0 121122 2 0 121123 1 0 123124 1 0 124125 1 0 125126 1 0 124127 1 0 127128 1 0 128129 2 0 129130 1 0 130131 2 0 131132 1 0 132133 2 0 90134 1 0 134135 1 0 134136 1 0 55137 1 0 137138 1 0 137139 1 0 14 10 1 0 86 82 1 0 133128 1 0 1140 1 0 1141 1 0 1142 1 0 4143 1 0 6144 1 0 6145 1 0 6146 1 0 7147 1 0 7148 1 0 7149 1 0 11150 1 0 11151 1 0 12152 1 0 12153 1 0 13154 1 0 13155 1 0 14156 1 1 17157 1 0 19158 1 0 19159 1 0 19160 1 0 20161 1 0 20162 1 0 20163 1 0 23164 1 0 24165 1 6 25166 1 0 25167 1 0 25168 1 0 28169 1 0 30170 1 0 30171 1 0 30172 1 0 31173 1 0 31174 1 0 31175 1 0 34176 1 0 35177 1 1 36178 1 0 36179 1 0 36180 1 0 39181 1 0 40182 1 6 41183 1 0 41184 1 0 42185 1 0 42186 1 0 44187 1 0 44188 1 0 48189 1 0 50190 1 0 50191 1 0 50192 1 0 51193 1 0 51194 1 0 51195 1 0 54196 1 0 55197 1 1 58198 1 0 60199 1 0 60200 1 0 60201 1 0 61202 1 0 61203 1 0 61204 1 0 64205 1 0 65206 1 0 65207 1 0 68208 1 0 69209 1 1 70210 1 0 70211 1 0 71212 1 0 72213 1 0 72214 1 0 72215 1 0 73216 1 0 73217 1 0 73218 1 0 76219 1 0 78220 1 0 78221 1 0 78222 1 0 79223 1 0 79224 1 0 79225 1 0 83226 1 0 83227 1 0 84228 1 0 84229 1 0 85230 1 0 85231 1 0 86232 1 1 89233 1 0 90234 1 6 93235 1 0 95236 1 0 95237 1 0 95238 1 0 96239 1 0 96240 1 0 96241 1 0 99242 1 0 101243 1 0 101244 1 0 101245 1 0 102246 1 0 102247 1 0 102248 1 0 105249 1 0 106250 1 6 107251 1 0 107252 1 0 108253 1 0 108254 1 0 110255 1 0 110256 1 0 114257 1 0 115258 1 1 116259 1 0 116260 1 0 117261 1 0 117262 1 0 119263 1 0 119264 1 0 123265 1 0 124266 1 6 125267 1 0 125268 1 0 126269 1 0 127270 1 0 127271 1 0 129272 1 0 130273 1 0 131274 1 0 132275 1 0 133276 1 0 134277 1 0 135278 1 0 135279 1 0 135280 1 0 136281 1 0 136282 1 0 136283 1 0 137284 1 0 138285 1 0 138286 1 0 138287 1 0 139288 1 0 139289 1 0 139290 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 NPC611827 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	26943
0.1-0.2	22001
0.2-0.3	671
0.3-0.4	170
0.4-0.5	37
0.5-0.6	15
0.6-0.7	11
0.7-0.8	0
0.8-0.85	1
0.85-0.9	3
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9	High Similarity	NPC602086
0.8911	High Similarity	NPC604070
0.8824	High Similarity	NPC607051
0.8824	High Similarity	NPC607671
0.8396	Intermediate Similarity	NPC605521
0.7982	Intermediate Similarity	NPC600030
0.75	Intermediate Similarity	NPC601101
0.7129	Intermediate Similarity	NPC604834
0.7129	Intermediate Similarity	NPC605449
0.6979	Remote Similarity	NPC607611
0.686	Remote Similarity	NPC600031
0.6634	Remote Similarity	NPC601100
0.6609	Remote Similarity	NPC608940
0.6574	Remote Similarity	NPC606448
0.641	Remote Similarity	NPC601005
0.6261	Remote Similarity	NPC610887
0.6068	Remote Similarity	NPC602163
0.6058	Remote Similarity	NPC610465
0.605	Remote Similarity	NPC600509
0.6031	Remote Similarity	NPC602884
0.5981	Remote Similarity	NPC608010
0.5868	Remote Similarity	NPC605605
0.5841	Remote Similarity	NPC606241
0.5809	Remote Similarity	NPC605005
0.5809	Remote Similarity	NPC610934
0.5735	Remote Similarity	NPC609932
0.5701	Remote Similarity	NPC600037
0.5571	Remote Similarity	NPC606456
0.5571	Remote Similarity	NPC606896
0.5556	Remote Similarity	NPC601044
0.5446	Remote Similarity	NPC477539
0.5421	Remote Similarity	NPC599967
0.5321	Remote Similarity	NPC606504
0.5225	Remote Similarity	NPC601391
0.5089	Remote Similarity	NPC600368

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611827 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4292
0.1-0.2	4802
0.2-0.3	56
0.3-0.4	0
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