NPASS Compound

Natural Product: NPC472200

Natural Product ID	NPC472200
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VZCOSHRWLFNASZ-IMDRUOPXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3344504
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

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

Chemical Representations

RDKit 2D 182187 0 0 0 0 0 0 0 0999 V2000 5.4596 4.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0294 2.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5992 1.5347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1690 0.0977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7388 -1.3393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3086 -2.7762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0586 -4.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3191 -5.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0586 -7.0297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3086 -8.3287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 -9.2929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -9.8060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -9.8060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1595 -9.2929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3086 -8.3287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0586 -7.0297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4681 -7.5427 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3191 -5.5525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0586 -4.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3086 -2.7762 0.0000 C 0 0 0 0 0 0 0 0 0 0 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0 0 -14.5958 1.8121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.3458 0.5130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.5958 -0.7860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.3354 -2.2632 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -16.4949 -0.4512 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -16.0054 2.3251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.0958 -3.7404 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.3563 -2.2632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.7658 -2.7762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -15.9149 -1.8121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -17.3244 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.6544 -0.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.2449 0.1782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.0958 -0.7860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.6863 -1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.0958 1.1424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -15.9149 1.1424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -17.3244 1.6554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -18.4735 0.6912 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -17.5849 3.1326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 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0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 28 34 1 0 20 35 1 0 35 36 1 0 36 37 1 0 36 38 1 0 38 39 1 0 39 40 1 0 38 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 44 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 2 0 50 52 1 0 52 53 1 0 53 54 1 0 52 55 1 0 47 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 59 60 1 0 60 61 1 0 59 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 63 66 1 0 62 67 1 0 46 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 71 72 1 0 71 73 1 0 73 74 1 0 74 75 1 0 75 76 1 0 74 77 1 0 73 78 1 0 78 79 1 0 79 80 2 0 79 81 1 0 81 82 1 0 82 83 1 0 81 84 1 0 24 6 1 0 48 42 1 0 64 57 1 0 75 69 1 0 39 19 1 0 29 22 1 0 1 85 1 0 1 86 1 0 1 87 1 0 2 88 1 0 2 89 1 0 3 90 1 0 3 91 1 0 4 92 1 0 4 93 1 0 5 94 1 0 5 95 1 0 6 96 1 6 7 97 1 0 7 98 1 0 8 99 1 0 8100 1 0 9101 1 0 9102 1 0 10103 1 0 10104 1 0 11105 1 0 11106 1 0 12107 1 0 12108 1 0 13109 1 0 13110 1 0 14111 1 0 14112 1 0 15113 1 0 15114 1 0 19115 1 1 20116 1 6 22117 1 1 23118 1 6 26119 1 6 27120 1 0 27121 1 0 27122 1 0 28123 1 6 29124 1 6 33125 1 0 33126 1 0 33127 1 0 34128 1 0 36129 1 1 37130 1 0 37131 1 0 37132 1 0 38133 1 6 39134 1 1 40135 1 0 42136 1 1 44137 1 6 45138 1 0 45139 1 0 45140 1 0 46141 1 1 47142 1 6 48143 1 6 52144 1 6 53145 1 0 53146 1 0 54147 1 0 54148 1 0 54149 1 0 55150 1 0 55151 1 0 55152 1 0 57153 1 6 59154 1 6 60155 1 0 60156 1 0 61157 1 0 62158 1 1 63159 1 6 64160 1 1 65161 1 0 66162 1 0 67163 1 0 69164 1 1 71165 1 6 72166 1 0 72167 1 0 72168 1 0 73169 1 1 74170 1 6 75171 1 6 76172 1 0 77173 1 0 81174 1 6 82175 1 0 82176 1 0 83177 1 0 83178 1 0 83179 1 0 84180 1 0 84181 1 0 84182 1 0 M END

Standard InCHIKey	VZCOSHRWLFNASZ-IMDRUOPXSA-N
Standard InCHI	InChI=1S/C58H98O26/c1-11-14-20-23-34-24-21-18-16-15-17-19-22-25-36(61)78-48-43(68)45(31(8)73-56(48)84-50-47(75-33(10)60)37(62)29(6)71-57(50)76-34)81-58-51(80-53(70)28(5)13-3)49(83-55-41(66)39(64)38(63)35(26-59)77-55)46(32(9)74-58)82-54-42(67)40(65)44(30(7)72-54)79-52(69)27(4)12-2/h27-32,34-35,37-51,54-59,62-68H,11-26H2,1-10H3/t27-,28-,29+,30-,31-,32-,34-,35+,37-,38+,39-,40-,41+,42+,43+,44-,45-,46-,47-,48+,49+,50+,51+,54-,55-,56-,57-,58-/m0/s1
SMILES	CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@H](O[C@H]3[C@H](O1)O[C@H](C)[C@@H]([C@@H]3OC(=O)C)O)O[C@@H](C)[C@@H]([C@H]2O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)[C@H](CC)C)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)OC(=O)[C@H](CC)C

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
NPO33128	merremia hederacea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25310730]

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
Ratio IC50	1
IC50	1

Activity Type	# Activity
Others	2

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
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	2.3	n.a.	PMID[20405844]
NPT2	Others	Unspecified	n.a.	IC50	=	253.0	nM	PMID[20405844]

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 NPC472200 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	22133
0.1-0.2	23824
0.2-0.3	3530
0.3-0.4	223
0.4-0.5	36
0.5-0.6	48
0.6-0.7	46
0.7-0.8	0
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8795	High Similarity	NPC477317
0.8795	High Similarity	NPC477318
0.869	High Similarity	NPC224953
0.8256	Intermediate Similarity	NPC184915
0.8068	Intermediate Similarity	NPC44782
0.7907	Intermediate Similarity	NPC119583
0.7727	Intermediate Similarity	NPC115013
0.7558	Intermediate Similarity	NPC109887
0.7444	Intermediate Similarity	NPC126685
0.7416	Intermediate Similarity	NPC483170
0.7326	Intermediate Similarity	NPC478734
0.7326	Intermediate Similarity	NPC89843
0.7273	Intermediate Similarity	NPC478722
0.7253	Intermediate Similarity	NPC183888
0.7159	Intermediate Similarity	NPC478733
0.7126	Intermediate Similarity	NPC477331
0.7045	Intermediate Similarity	NPC477344
0.7	Intermediate Similarity	NPC297768
0.6957	Remote Similarity	NPC169345
0.6882	Remote Similarity	NPC259294
0.6848	Remote Similarity	NPC478726
0.6739	Remote Similarity	NPC143421
0.6739	Remote Similarity	NPC472204
0.6705	Remote Similarity	NPC22742
0.6705	Remote Similarity	NPC477346
0.6703	Remote Similarity	NPC146992
0.6703	Remote Similarity	NPC85759
0.6667	Remote Similarity	NPC238264
0.6667	Remote Similarity	NPC477345
0.663	Remote Similarity	NPC477319
0.6602	Remote Similarity	NPC290276
0.6596	Remote Similarity	NPC290012
0.6559	Remote Similarity	NPC307400
0.6559	Remote Similarity	NPC27289
0.6559	Remote Similarity	NPC294748
0.6552	Remote Similarity	NPC477328
0.6484	Remote Similarity	NPC477326
0.6484	Remote Similarity	NPC600446
0.6484	Remote Similarity	NPC605013
0.6471	Remote Similarity	NPC478729
0.6452	Remote Similarity	NPC472205
0.6452	Remote Similarity	NPC478723
0.6421	Remote Similarity	NPC238056
0.6374	Remote Similarity	NPC477332
0.6344	Remote Similarity	NPC478725
0.63	Remote Similarity	NPC475241
0.6289	Remote Similarity	NPC123204
0.6277	Remote Similarity	NPC478724
0.618	Remote Similarity	NPC477330
0.6174	Remote Similarity	NPC147032
0.6162	Remote Similarity	NPC478728
0.6146	Remote Similarity	NPC476087
0.6146	Remote Similarity	NPC475667
0.6129	Remote Similarity	NPC479059
0.6126	Remote Similarity	NPC471024
0.6111	Remote Similarity	NPC477329
0.61	Remote Similarity	NPC478727
0.6082	Remote Similarity	NPC478732
0.602	Remote Similarity	NPC475270
0.602	Remote Similarity	NPC475327
0.6	Remote Similarity	NPC77651
0.6	Remote Similarity	NPC479061
0.6	Remote Similarity	NPC267592
0.6	Remote Similarity	NPC600940
0.5981	Remote Similarity	NPC611287
0.5946	Remote Similarity	NPC472352
0.5938	Remote Similarity	NPC479060
0.5934	Remote Similarity	NPC281563
0.5914	Remote Similarity	NPC604005
0.5914	Remote Similarity	NPC605014
0.5849	Remote Similarity	NPC28069
0.5833	Remote Similarity	NPC10883
0.5806	Remote Similarity	NPC113745
0.5806	Remote Similarity	NPC477320
0.5806	Remote Similarity	NPC477323
0.5806	Remote Similarity	NPC477325
0.5806	Remote Similarity	NPC609436
0.578	Remote Similarity	NPC610996
0.5778	Remote Similarity	NPC477350
0.5743	Remote Similarity	NPC269318
0.573	Remote Similarity	NPC606819
0.5727	Remote Similarity	NPC471025
0.5686	Remote Similarity	NPC475164
0.5636	Remote Similarity	NPC600672
0.5612	Remote Similarity	NPC173328
0.5556	Remote Similarity	NPC478730
0.5545	Remote Similarity	NPC10121
0.5545	Remote Similarity	NPC198918
0.5536	Remote Similarity	NPC600721
0.5536	Remote Similarity	NPC605872
0.5526	Remote Similarity	NPC471026
0.551	Remote Similarity	NPC60849
0.549	Remote Similarity	NPC163409
0.5481	Remote Similarity	NPC473605
0.5481	Remote Similarity	NPC475375
0.5474	Remote Similarity	NPC477349
0.5464	Remote Similarity	NPC158302
0.5455	Remote Similarity	NPC479058
0.5439	Remote Similarity	NPC610997
0.5437	Remote Similarity	NPC477347
0.54	Remote Similarity	NPC186992
0.5376	Remote Similarity	NPC146380
0.5294	Remote Similarity	NPC478731
0.5283	Remote Similarity	NPC477348
0.5192	Remote Similarity	NPC475525
0.5192	Remote Similarity	NPC475540
0.5182	Remote Similarity	NPC63404
0.5143	Remote Similarity	NPC476066
0.5096	Remote Similarity	NPC479057
0.5045	Remote Similarity	NPC35338
0.5045	Remote Similarity	NPC204214
0.5045	Remote Similarity	NPC92283

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472200 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7258
0.1-0.2	1816
0.2-0.3	74
0.3-0.4	2
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