NPASS Compound

Natural Product: NPC480596

Natural Product ID	NPC480596
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DMJBZSFNVSAWKO-GSMQILRFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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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133383 1 0 134384 1 0 135385 1 0 136386 1 0 139387 1 1 140388 1 0 140389 1 0 141390 1 0 141391 1 0 142392 1 0 142393 1 0 143394 1 0 143395 1 0 144396 1 0 144397 1 0 145398 1 0 145399 1 0 146400 1 0 149401 1 6 150402 1 0 150403 1 0 151404 1 0 154405 1 0 154406 1 0 157407 1 1 158408 1 0 158409 1 0 158410 1 0 161411 1 0 162412 1 0 163413 1 0 164414 1 0 165415 1 0 168416 1 1 169417 1 0 169418 1 0 170419 1 0 170420 1 0 172421 1 0 173422 1 0 176423 1 1 177424 1 0 177425 1 0 178426 1 0 178427 1 0 181428 1 0 184429 1 6 185430 1 0 185431 1 0 186432 1 0 186433 1 0 187434 1 0 187435 1 0 191436 1 1 192437 1 0 192438 1 0 193439 1 0 193440 1 0 194441 1 0 194442 1 0 198443 1 0 198444 1 0 201445 1 1 202446 1 0 202447 1 0 204448 1 0 205449 1 0 206450 1 0 207451 1 0 208452 1 0 211453 1 0 211454 1 0 214455 1 1 215456 1 0 215457 1 0 216458 1 0 219459 1 0 220460 1 0 221461 1 0 222462 1 0 223463 1 0 224464 1 0 225465 1 0 228466 1 1 229467 1 0 229468 1 0 230469 1 0 230470 1 0 232471 1 0 233472 1 0 236473 1 0 237474 1 0 238475 1 0 239476 1 0 240477 1 0 241478 1 0 242479 1 0 243480 1 0 244481 1 0 245482 1 0 246483 1 0 247484 1 0 M END

Standard InCHIKey	DMJBZSFNVSAWKO-GSMQILRFSA-N
Standard InCHI	InChI=1S/C154H237N43O44S6/c1-15-79(10)120-148(235)187-104-73-246-247-74-105-140(227)189-119(78(8)9)152(239)197-55-30-40-108(197)142(229)177-95(59-86-60-161-75-167-86)149(236)194-52-28-41-109(194)144(231)192-122(81(12)17-3)147(234)175-92(56-76(4)5)133(220)171-88(37-26-50-162-154(159)160)132(219)191-121(80(11)16-2)146(233)176-94(58-85-34-22-19-23-35-85)134(221)188-118(77(6)7)145(232)186-103(135(222)174-91(153(240)241)44-47-112(158)203)72-245-244-71-102(184-131(218)89(43-46-111(157)202)172-130(217)90(45-48-117(208)209)173-141(228)107-39-29-54-196(107)151(238)110-42-31-51-193(110)116(207)64-166-126(213)93(57-84-32-20-18-21-33-84)170-115(206)63-165-128(215)97(66-199)179-137(104)224)139(226)185-101(136(223)178-96(65-198)127(214)163-61-113(204)168-82(13)123(210)182-105)70-243-242-69-100(183-125(212)87(156)36-24-25-49-155)138(225)181-99(68-201)150(237)195-53-27-38-106(195)143(230)180-98(67-200)129(216)164-62-114(205)169-83(14)124(211)190-120/h18-23,32-35,60,75-83,87-110,118-122,198-201H,15-17,24-31,36-59,61-74,155-156H2,1-14H3,(H2,157,202)(H2,158,203)(H,161,167)(H,163,214)(H,164,216)(H,165,215)(H,166,213)(H,168,204)(H,169,205)(H,170,206)(H,171,220)(H,172,217)(H,173,228)(H,174,222)(H,175,234)(H,176,233)(H,177,229)(H,178,223)(H,179,224)(H,180,230)(H,181,225)(H,182,210)(H,183,212)(H,184,218)(H,185,226)(H,186,232)(H,187,235)(H,188,221)(H,189,227)(H,190,211)(H,191,219)(H,192,231)(H,208,209)(H,240,241)(H4,159,160,162)/t79-,80-,81-,82-,83-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,107-,108-,109-,110-,118-,119-,120-,121-,122-/m0/s1
SMILES	CC[C@H](C)[C@H]1C(=N[C@H]2CSSC[C@H]3C(=N[C@@H](C(C)C)C(=O)N4CCC[C@H]4C(=N[C@@H](Cc4cnc[nH]4)C(=O)N4CCC[C@H]4C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](CC(C)C)C(=N[C@@H](CCCNC(=N)N)C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](Cc4ccccc4)C(=N[C@@H](C(C)C)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](CO)C(=O)N4CCC[C@H]4C(=N[C@@H](CO)C(=NCC(=N[C@@H](C)C(=N1)O)O)O)O)O)N=C([C@H](CCCCN)N)O)C(=N[C@@H](CO)C(=NCC(=N[C@@H](C)C(=N3)O)O)O)O)O)N=C([C@H](CCC(=N)O)N=C([C@H](CCC(=O)O)N=C([C@@H]1CCCN1C(=O)[C@@H]1CCCN1C(=O)CN=C([C@H](Cc1ccccc1)N=C(CN=C([C@H](CO)N=C2O)O)O)O)O)O)O)C(=N[C@@H](CCC(=N)O)C(=O)O)O)O)O)O)O)O)O)O)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
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.procbio.2005.03.071]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1023/A:1011684619614]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33118348]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36432211]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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
Activity	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
NPT1568	Individual protein	Trypsin I	Bos taurus	Activity	=	185.0	nM	PMID[33118348]

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 NPC480596 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	33045
0.1-0.2	16004
0.2-0.3	555
0.3-0.4	160
0.4-0.5	51
0.5-0.6	37
0.6-0.7	4
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
0.7156	Intermediate Similarity	NPC480595
0.6498	Remote Similarity	NPC480594
0.6091	Remote Similarity	NPC484365
0.6051	Remote Similarity	NPC485115
0.602	Remote Similarity	NPC484363
0.598	Remote Similarity	NPC484964
0.5969	Remote Similarity	NPC486507
0.595	Remote Similarity	NPC489217
0.5939	Remote Similarity	NPC486505
0.5894	Remote Similarity	NPC480440
0.5859	Remote Similarity	NPC477632
0.5808	Remote Similarity	NPC484963
0.5708	Remote Similarity	NPC489215
0.5682	Remote Similarity	NPC479082
0.5673	Remote Similarity	NPC477635
0.5619	Remote Similarity	NPC486506
0.5619	Remote Similarity	NPC485247
0.5619	Remote Similarity	NPC486514
0.5594	Remote Similarity	NPC484078
0.5581	Remote Similarity	NPC477634
0.5545	Remote Similarity	NPC485246
0.5545	Remote Similarity	NPC482981
0.5535	Remote Similarity	NPC477633
0.5532	Remote Similarity	NPC484882
0.552	Remote Similarity	NPC479083
0.5515	Remote Similarity	NPC485114
0.5514	Remote Similarity	NPC489216
0.5512	Remote Similarity	NPC485243
0.5484	Remote Similarity	NPC329843
0.5405	Remote Similarity	NPC489512
0.5381	Remote Similarity	NPC485242
0.5366	Remote Similarity	NPC485245
0.536	Remote Similarity	NPC486517
0.5343	Remote Similarity	NPC484364
0.5325	Remote Similarity	NPC479872
0.53	Remote Similarity	NPC479136
0.5283	Remote Similarity	NPC484362
0.5259	Remote Similarity	NPC480533
0.5189	Remote Similarity	NPC483294
0.5179	Remote Similarity	NPC485116
0.5139	Remote Similarity	NPC489511
0.5106	Remote Similarity	NPC479143

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC480596 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4523
0.1-0.2	4503
0.2-0.3	112
0.3-0.4	10
0.4-0.5	2
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