NPASS Compound

Natural Product: NPC472352

Natural Product ID	NPC472352
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	QHWDTDHKZFTJKU-XPHXFLJASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3360736
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

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0 115248 1 0 115249 1 0 116250 1 0 116251 1 0 116252 1 0 117253 1 0 M END

Standard InCHIKey	QHWDTDHKZFTJKU-XPHXFLJASA-N
Standard InCHI	InChI=1S/C80H136O37/c1-13-17-18-19-20-21-22-26-29-33-49(83)109-64-53(87)41(9)101-75(61(64)95)113-63-43(11)104-79(71(112-73(98)38(6)16-4)69(63)116-78-68(59(93)55(89)47(35-81)107-78)114-76-62(96)65(54(88)42(10)102-76)111-72(97)37(5)15-3)117-70-66-56(90)48(36-99-44(12)82)108-80(70)115-67-58(92)52(86)40(8)103-77(67)105-45(30-14-2)31-27-24-23-25-28-32-46(34-50(84)110-66)106-74-60(94)57(91)51(85)39(7)100-74/h37-43,45-48,51-71,74-81,85-96H,13-36H2,1-12H3/t37-,38-,39+,40+,41+,42+,43-,45+,46-,47+,48+,51+,52+,53-,54+,55+,56+,57-,58-,59-,60+,61+,62+,63-,64-,65-,66-,67+,68+,69+,70+,71+,74-,75-,76-,77-,78-,79-,80-/m0/s1
SMILES	CCCCCCCCCCCC(=O)OC1C(C(OC(C1O)OC2C(OC(C(C2OC3C(C(C(C(O3)CO)O)O)OC4C(C(C(C(O4)C)O)OC(=O)C(C)CC)O)OC(=O)C(C)CC)OC5C6C(C(OC5OC7C(C(C(OC7OC(CCCCCCCC(CC(=O)O6)OC8C(C(C(C(O8)C)O)O)O)CCC)C)O)O)COC(=O)C)O)C)C)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
NPO33226	ipomea purga	Species	n.a.	n.a.	resin glycosides	n.a.	n.a.	PMID[25536852]

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	3
FC	3

Activity Type	# Activity
Cell line	6

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
NPT83	Cell line	MCF7	Homo sapiens	IC50	<	0.00064	ug.mL-1	DrugMatrix in vivo data: Hematology
NPT83	Cell line	MCF7	Homo sapiens	FC	>	1593.0	n.a.	PubChem BioAssay data set
NPT83	Cell line	MCF7	Homo sapiens	FC	>	1906.3	n.a.	PubChem BioAssay data set
NPT83	Cell line	MCF7	Homo sapiens	FC	=	73.4	n.a.	PMID[24613627]

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 NPC472352 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	26064
0.1-0.2	20553
0.2-0.3	2755
0.3-0.4	362
0.4-0.5	24
0.5-0.6	66
0.6-0.7	32
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	Natural Product ID
0.6796	Remote Similarity	NPC472204
0.6768	Remote Similarity	NPC22742
0.6768	Remote Similarity	NPC477346
0.6765	Remote Similarity	NPC146992
0.6765	Remote Similarity	NPC85759
0.6667	Remote Similarity	NPC169345
0.6635	Remote Similarity	NPC294748
0.6538	Remote Similarity	NPC173328
0.6509	Remote Similarity	NPC238056
0.6481	Remote Similarity	NPC269318
0.6449	Remote Similarity	NPC259294
0.6449	Remote Similarity	NPC126685
0.6408	Remote Similarity	NPC158302
0.6381	Remote Similarity	NPC477319
0.6321	Remote Similarity	NPC143421
0.6321	Remote Similarity	NPC186992
0.6296	Remote Similarity	NPC183888
0.6296	Remote Similarity	NPC184915
0.6204	Remote Similarity	NPC290012
0.6182	Remote Similarity	NPC44782
0.6168	Remote Similarity	NPC307400
0.6168	Remote Similarity	NPC27289
0.6154	Remote Similarity	NPC478734
0.6154	Remote Similarity	NPC89843
0.6147	Remote Similarity	NPC224953
0.6102	Remote Similarity	NPC611287
0.6058	Remote Similarity	NPC604005
0.6058	Remote Similarity	NPC605014
0.6055	Remote Similarity	NPC477317
0.6055	Remote Similarity	NPC477318
0.6038	Remote Similarity	NPC478733
0.6019	Remote Similarity	NPC119583
0.5963	Remote Similarity	NPC483170
0.5963	Remote Similarity	NPC476087
0.5963	Remote Similarity	NPC475667
0.5946	Remote Similarity	NPC472200
0.5946	Remote Similarity	NPC123204
0.5943	Remote Similarity	NPC477344
0.5941	Remote Similarity	NPC477350
0.5926	Remote Similarity	NPC297768
0.5909	Remote Similarity	NPC478732
0.5909	Remote Similarity	NPC115013
0.5856	Remote Similarity	NPC475270
0.5856	Remote Similarity	NPC475327
0.5818	Remote Similarity	NPC238264
0.5818	Remote Similarity	NPC477345
0.5794	Remote Similarity	NPC477326
0.5728	Remote Similarity	NPC475425
0.5728	Remote Similarity	NPC146380
0.5702	Remote Similarity	NPC475164
0.5688	Remote Similarity	NPC267592
0.5664	Remote Similarity	NPC163409
0.566	Remote Similarity	NPC113745
0.566	Remote Similarity	NPC477349
0.566	Remote Similarity	NPC477320
0.566	Remote Similarity	NPC477323
0.566	Remote Similarity	NPC477325
0.566	Remote Similarity	NPC609436
0.5656	Remote Similarity	NPC600672
0.5636	Remote Similarity	NPC44682
0.56	Remote Similarity	NPC600940
0.5596	Remote Similarity	NPC109887
0.5565	Remote Similarity	NPC600721
0.5565	Remote Similarity	NPC605872
0.5556	Remote Similarity	NPC477331
0.5517	Remote Similarity	NPC473605
0.5517	Remote Similarity	NPC475375
0.5505	Remote Similarity	NPC600446
0.5505	Remote Similarity	NPC605013
0.55	Remote Similarity	NPC63404
0.5446	Remote Similarity	NPC478730
0.5372	Remote Similarity	NPC35338
0.5372	Remote Similarity	NPC204214
0.5372	Remote Similarity	NPC92283
0.5357	Remote Similarity	NPC472205
0.5351	Remote Similarity	NPC478731
0.5323	Remote Similarity	NPC10121
0.5323	Remote Similarity	NPC198918
0.5323	Remote Similarity	NPC290276
0.528	Remote Similarity	NPC610996
0.5268	Remote Similarity	NPC478722
0.5263	Remote Similarity	NPC478726
0.5259	Remote Similarity	NPC475525
0.5259	Remote Similarity	NPC475540
0.5214	Remote Similarity	NPC476066
0.5185	Remote Similarity	NPC281563
0.5185	Remote Similarity	NPC477329
0.5167	Remote Similarity	NPC475241
0.5143	Remote Similarity	NPC478729
0.5093	Remote Similarity	NPC477328
0.5093	Remote Similarity	NPC477330
0.5088	Remote Similarity	NPC479058
0.5081	Remote Similarity	NPC28069
0.5079	Remote Similarity	NPC10883
0.5074	Remote Similarity	NPC147032
0.5043	Remote Similarity	NPC479057
0.5041	Remote Similarity	NPC124878
0.5041	Remote Similarity	NPC231888

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472352 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7524
0.1-0.2	1566
0.2-0.3	58
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