NPASS Compound

Natural Product: NPC481324

Natural Product ID	NPC481324
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	YWOGMCXCUIFEBS-QKPVQVBOSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44559171
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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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33 1 0 29 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 40 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 54 55 1 6 54 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 59 60 1 6 59 61 1 0 61 62 1 0 62 63 1 0 63 64 2 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 67 69 1 0 67 70 1 0 70 71 1 0 71 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 75 76 1 1 72 77 1 6 77 78 2 0 77 79 1 0 79 80 1 0 80 81 1 0 81 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 1 0 88 89 1 0 89 90 1 0 90 91 1 0 91 92 1 0 92 93 1 0 91 94 1 0 90 95 1 0 95 96 1 0 96 97 1 0 97 98 1 0 98 99 1 0 99100 1 0 100101 1 0 100102 1 0 99103 1 0 98104 1 0 97105 1 0 89106 1 0 88107 1 0 84108 1 0 83109 1 0 82110 1 0 81111 1 0 56112 1 0 112113 1 0 112114 1 0 46115 1 0 45116 1 0 36117 1 0 17118 1 0 12119 1 0 119120 1 0 120121 2 0 120122 1 0 122123 2 0 123124 1 0 124125 2 0 125126 1 0 126127 2 0 127128 1 0 128129 2 0 128130 1 0 130131 1 0 127132 1 0 11133 1 0 10134 1 0 6135 1 0 5136 1 0 4137 1 0 3138 1 0 135 2 1 0 14 9 1 0 23 16 1 0 31 26 1 0 41 35 1 0 49 44 1 0 112 51 1 0 129124 1 0 61 54 1 0 75 64 1 0 108 80 1 0 75 59 1 0 94 87 1 0 102 96 1 0 72 65 1 0 1139 1 0 1140 1 0 1141 1 0 2142 1 1 3143 1 6 4144 1 1 5145 1 1 6146 1 6 8147 1 0 8148 1 0 9149 1 6 10150 1 1 11151 1 6 12152 1 1 13153 1 6 16154 1 6 17155 1 1 18156 1 6 19157 1 0 19158 1 0 20159 1 0 22160 1 6 23161 1 1 24162 1 0 26163 1 1 27164 1 0 27165 1 0 29166 1 6 30167 1 1 31168 1 1 32169 1 0 33170 1 0 35171 1 1 36172 1 6 37173 1 1 38174 1 0 38175 1 0 38176 1 0 40177 1 6 41178 1 1 42179 1 0 44180 1 6 45181 1 1 46182 1 1 47183 1 0 47184 1 0 49185 1 1 51186 1 1 52187 1 0 52188 1 0 53189 1 0 53190 1 0 55191 1 0 55192 1 0 55193 1 0 56194 1 1 57195 1 0 57196 1 0 58197 1 0 58198 1 0 60199 1 0 60200 1 0 60201 1 0 61202 1 1 62203 1 0 62204 1 0 63205 1 0 65206 1 6 66207 1 0 66208 1 0 68209 1 0 68210 1 0 68211 1 0 69212 1 0 69213 1 0 69214 1 0 70215 1 0 70216 1 0 71217 1 0 71218 1 0 73219 1 0 73220 1 0 74221 1 0 74222 1 0 76223 1 0 76224 1 0 76225 1 0 80226 1 1 81227 1 6 82228 1 1 83229 1 6 84230 1 1 85231 1 0 85232 1 0 87233 1 1 88234 1 6 89235 1 1 90236 1 6 91237 1 1 92238 1 0 92239 1 0 93240 1 0 96241 1 1 97242 1 6 98243 1 6 99244 1 1 100245 1 6 101246 1 0 101247 1 0 101248 1 0 103249 1 0 104250 1 0 105251 1 0 106252 1 0 107253 1 0 109254 1 0 110255 1 0 111256 1 0 113257 1 0 113258 1 0 113259 1 0 114260 1 0 114261 1 0 114262 1 0 115263 1 0 116264 1 0 117265 1 0 118266 1 0 122267 1 0 123268 1 0 125269 1 0 126270 1 0 129271 1 0 131272 1 0 131273 1 0 131274 1 0 132275 1 0 133276 1 0 134277 1 0 136278 1 0 137279 1 0 138280 1 0 M END

Standard InCHIKey	YWOGMCXCUIFEBS-QKPVQVBOSA-N
Standard InCHI	InChI=1S/C92H142O46/c1-34-52(98)60(106)66(112)77(124-34)121-32-46-57(103)63(109)76(133-51(97)17-13-37-12-15-40(95)42(26-37)119-11)85(131-46)136-74-59(105)43(28-93)127-83(71(74)117)130-47-33-123-79(65(111)58(47)104)135-73-54(100)36(3)126-82(70(73)116)137-75-55(101)41(96)30-120-84(75)132-50-19-20-89(8)48(88(50,6)7)18-21-91(10)49(89)16-14-38-39-27-87(4,5)22-24-92(39,25-23-90(38,91)9)86(118)138-81-68(114)62(108)56(102)45(129-81)31-122-78-69(115)64(110)72(44(29-94)128-78)134-80-67(113)61(107)53(99)35(2)125-80/h12-15,17,26,34-36,39,41,43-50,52-85,93-96,98-117H,16,18-25,27-33H2,1-11H3/b17-13+/t34-,35-,36-,39-,41-,43+,44+,45+,46+,47+,48-,49+,50-,52-,53-,54-,55-,56+,57+,58+,59+,60+,61+,62-,63-,64+,65+,66+,67+,68+,69+,70+,71+,72+,73+,74-,75+,76+,77+,78+,79-,80-,81-,82-,83-,84-,85-,89-,90+,91+,92-/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)O[C@H]2[C@@H]([C@@H](CO)O[C@H]([C@@H]2O)O[C@@H]2CO[C@H]([C@@H]([C@@H]2O)O)O[C@@H]2[C@H]([C@H](C)O[C@H]([C@@H]2O)O[C@@H]2[C@H]([C@H](CO[C@H]2O[C@H]2CC[C@@]3(C)[C@@H](CC[C@]4(C)[C@@H]3CC=C3[C@@H]5CC(C)(C)CC[C@@]5(CC[C@@]43C)C(=O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]4[C@@H]([C@H]([C@@H]([C@@H](CO)O4)O[C@H]4[C@@H]([C@@H]([C@H]([C@H](C)O4)O)O)O)O)O)O3)O)O)O)C2(C)C)O)O)O)O)OC(=O)/C=C/c2ccc(c(c2)OC)O)O)O)O1)O)O)O

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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT581	Individual protein	Cyclooxygenase-2	Mus musculus	IC50	=	2580.0	nM	PMID[17125227]

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 NPC481324 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	15844
0.1-0.2	30087
0.2-0.3	2839
0.3-0.4	748
0.4-0.5	247
0.5-0.6	40
0.6-0.7	30
0.7-0.8	0
0.8-0.85	4
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8667	High Similarity	NPC32723
0.8609	High Similarity	NPC481323
0.8609	High Similarity	NPC469778
0.8377	Intermediate Similarity	NPC135334
0.8228	Intermediate Similarity	NPC295941
0.8224	Intermediate Similarity	NPC469776
0.8182	Intermediate Similarity	NPC469774
0.7911	Intermediate Similarity	NPC100925
0.7812	Intermediate Similarity	NPC469777
0.7778	Intermediate Similarity	NPC469772
0.7756	Intermediate Similarity	NPC469775
0.7576	Intermediate Similarity	NPC469773
0.75	Intermediate Similarity	NPC261506
0.75	Intermediate Similarity	NPC4328
0.7431	Intermediate Similarity	NPC305981
0.731	Intermediate Similarity	NPC236638
0.731	Intermediate Similarity	NPC294453
0.7292	Intermediate Similarity	NPC41061
0.7292	Intermediate Similarity	NPC227551
0.7027	Intermediate Similarity	NPC298034
0.7027	Intermediate Similarity	NPC71065
0.6901	Remote Similarity	NPC60557
0.6901	Remote Similarity	NPC67857
0.6892	Remote Similarity	NPC43550
0.6887	Remote Similarity	NPC250247
0.6875	Remote Similarity	NPC135904
0.6846	Remote Similarity	NPC202828
0.6846	Remote Similarity	NPC119592
0.6736	Remote Similarity	NPC79643
0.6622	Remote Similarity	NPC481080
0.6601	Remote Similarity	NPC220160
0.6552	Remote Similarity	NPC475287
0.6533	Remote Similarity	NPC110633
0.6531	Remote Similarity	NPC123199
0.6447	Remote Similarity	NPC65105
0.6438	Remote Similarity	NPC76972
0.6438	Remote Similarity	NPC469782
0.6438	Remote Similarity	NPC204414
0.6358	Remote Similarity	NPC476068
0.6299	Remote Similarity	NPC481081
0.6242	Remote Similarity	NPC165204
0.6225	Remote Similarity	NPC488560
0.6164	Remote Similarity	NPC295823
0.6164	Remote Similarity	NPC174720
0.6164	Remote Similarity	NPC475467
0.6159	Remote Similarity	NPC475160
0.6159	Remote Similarity	NPC473714
0.6129	Remote Similarity	NPC293330
0.6122	Remote Similarity	NPC481078
0.609	Remote Similarity	NPC136768
0.6042	Remote Similarity	NPC63159
0.5975	Remote Similarity	NPC224381
0.5962	Remote Similarity	NPC258617
0.5924	Remote Similarity	NPC161717
0.5882	Remote Similarity	NPC155410
0.5833	Remote Similarity	NPC112352
0.5742	Remote Similarity	NPC100639
0.5733	Remote Similarity	NPC241909
0.5732	Remote Similarity	NPC57484
0.5667	Remote Similarity	NPC481079
0.566	Remote Similarity	NPC475514
0.5649	Remote Similarity	NPC192600
0.5617	Remote Similarity	NPC70809
0.557	Remote Similarity	NPC475504
0.5473	Remote Similarity	NPC104071
0.5436	Remote Similarity	NPC102439
0.54	Remote Similarity	NPC148417
0.5357	Remote Similarity	NPC480422
0.5329	Remote Similarity	NPC102505
0.5329	Remote Similarity	NPC488514
0.531	Remote Similarity	NPC48499
0.5304	Remote Similarity	NPC482013
0.5283	Remote Similarity	NPC219180
0.5283	Remote Similarity	NPC251263
0.5263	Remote Similarity	NPC297263
0.5257	Remote Similarity	NPC472268
0.525	Remote Similarity	NPC470218
0.5235	Remote Similarity	NPC469946
0.5232	Remote Similarity	NPC46665
0.52	Remote Similarity	NPC297950
0.5188	Remote Similarity	NPC475209
0.5181	Remote Similarity	NPC309223
0.5166	Remote Similarity	NPC160415
0.5132	Remote Similarity	NPC480475
0.5114	Remote Similarity	NPC40085
0.5099	Remote Similarity	NPC223301
0.5099	Remote Similarity	NPC171544
0.5096	Remote Similarity	NPC31838
0.5065	Remote Similarity	NPC222580
0.5054	Remote Similarity	NPC472269
0.5031	Remote Similarity	NPC54636

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC481324 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6001
0.1-0.2	3108
0.2-0.3	40
0.3-0.4	1
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