NPASS Compound

Natural Product: NPC608769

Natural Product ID	NPC608769
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DUGJJSWZRHBJJK-KLWPSQLOSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4851096
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

RDKit 3D 71 78 0 0 0 0 0 0 0 0999 V2000 -3.9299 0.4849 2.4075 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3908 0.4180 0.9706 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6129 -0.0049 0.1302 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1699 -0.0433 -1.2964 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1158 1.3311 -1.6986 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3482 2.1152 -0.8711 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9255 3.2390 -1.2660 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9521 1.7245 0.5333 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5208 2.1139 0.6639 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7465 1.4197 1.5418 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4371 0.1797 0.9325 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8985 0.1328 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8914 -0.7890 -0.4950 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5227 -0.7629 0.8856 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3192 -0.7611 1.7139 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9764 -1.2880 2.7294 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8559 -0.6441 -1.5711 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2065 0.1137 -2.7372 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0786 -1.9700 -2.0785 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2969 -2.8788 -1.4252 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3821 -4.1427 -1.4313 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2580 -2.1553 -0.6489 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0809 -2.7802 0.5603 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0107 -2.1278 -1.4612 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2383 -1.9404 -0.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5276 -0.5117 -0.2966 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0052 -0.1862 1.0735 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8058 0.8050 1.8411 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5301 1.8179 1.0251 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4014 2.5102 1.8682 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3019 1.2388 -0.1019 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8938 1.9205 -1.2747 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7819 1.3685 0.0339 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5033 0.7331 -1.0936 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9196 -0.1057 -1.9333 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5120 -0.4340 -1.7639 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8617 -0.8470 -2.7372 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9840 -0.2305 -0.3868 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7282 -1.1721 0.5119 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8294 -0.4727 2.9247 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9773 0.8597 2.3687 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3451 1.2984 2.9178 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3642 0.7758 0.2782 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9870 -0.9879 0.4837 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9380 -0.5027 -1.9553 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5284 2.4918 1.1470 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0021 2.0507 -0.3406 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4076 3.2099 0.9273 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1033 -1.6732 1.0596 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8490 -0.5482 -3.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9398 0.8142 -3.2015 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3902 0.7867 -2.3427 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5894 -3.6093 0.4516 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1065 -3.1249 -1.9520 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0111 -1.3760 -2.2478 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1577 -2.5597 0.3288 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0973 -2.3744 -1.1586 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0037 0.1671 -1.0112 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0512 -1.1508 1.6619 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0736 1.3783 2.4845 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5033 0.3484 2.5800 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7751 2.5905 0.6946 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6762 1.8931 2.5803 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6697 2.3009 -1.7481 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0053 2.4739 -0.0387 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1661 1.0679 1.0216 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5764 0.9716 -1.2386 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5105 -0.5324 -2.7356 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0296 -1.9437 0.9466 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2566 -0.7204 1.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4916 -1.7935 -0.0412 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 1 0 9 10 1 0 11 10 1 1 11 12 1 0 13 12 1 1 13 14 1 0 14 15 1 0 15 16 2 0 13 17 1 0 17 18 1 6 17 19 1 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 1 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 29 31 1 0 31 32 1 6 31 33 1 0 33 34 1 0 34 35 2 0 35 36 1 0 36 37 2 0 36 38 1 0 38 39 1 1 8 2 1 0 15 11 1 0 38 26 1 0 14 2 1 0 38 31 1 0 17 4 1 0 27 11 1 0 22 13 1 0 1 40 1 0 1 41 1 0 1 42 1 0 3 43 1 0 3 44 1 0 4 45 1 6 8 46 1 1 9 47 1 0 9 48 1 0 14 49 1 1 18 50 1 0 18 51 1 0 18 52 1 0 23 53 1 0 24 54 1 0 24 55 1 0 25 56 1 0 25 57 1 0 26 58 1 6 27 59 1 1 28 60 1 0 28 61 1 0 29 62 1 6 30 63 1 0 32 64 1 0 33 65 1 0 33 66 1 0 34 67 1 0 35 68 1 0 39 69 1 0 39 70 1 0 39 71 1 0 M END

Standard InCHIKey	DUGJJSWZRHBJJK-KLWPSQLOSA-N
Standard InCHI	InChI=1S/C28H32O11/c1-22-10-17-24(3)28-18(22)19(31)27(39-28,36-11-14(22)20(32)37-17)13-9-16(30)25(34)7-4-5-15(29)23(25,2)12(13)6-8-26(28,35)21(33)38-24/h4-5,12-14,16-18,30,34-35H,6-11H2,1-3H3/t12-,13+,14-,16+,17+,18-,22+,23-,24-,25-,26-,27+,28-/m0/s1
SMILES	C[C@@]12C[C@H]3OC(=O)[C@@H]1CO[C@]14O[C@@]5([C@H]2C1=O)[C@@]3(C)OC(=O)[C@@]5(O)CC[C@H]1[C@H]4C[C@@H](O)[C@@]2(O)CC=CC(=O)[C@]12C

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
NPO24001	Witheringia solanacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562828]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17580910]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21954931]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23270478]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25396337]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27295506]
NPO24001	Witheringia solanacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1161	Physalis minima	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1161	Physalis minima	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1161	Physalis minima	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1161	Physalis minima	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14304	Physalis alkekengi	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1161	Physalis minima	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24001	Witheringia solanacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14304	Physalis alkekengi	Species	Solanaceae	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
IC50	14
GI	10

Activity Type	# Activity
Cell line	24

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
NPT65	Cell line	HepG2	Homo sapiens	IC50	>	50000.0	nM	PMID[35608269]
NPT1374	Cell line	WI-38	Homo sapiens	GI	<	50.0	%	PMID[33586438]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	50000.0	nM	PMID[35608269]
NPT306	Cell line	PC-3	Homo sapiens	GI	<	50.0	%	PMID[33586438]
NPT81	Cell line	A549	Homo sapiens	IC50	>	50000.0	nM	PMID[35608269]
NPT83	Cell line	MCF7	Homo sapiens	GI	<	50.0	%	PMID[33586438]
NPT515	Cell line	SGC-7901	Homo sapiens	IC50	>	50000.0	nM	PMID[35608269]
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	49800.0	nM	PMID[35608269]
NPT397	Cell line	NCI-H460	Homo sapiens	GI	<	50.0	%	PMID[33586438]
NPT395	Cell line	SF-268	Homo sapiens	GI	<	50.0	%	PMID[33586438]
NPT113	Cell line	RAW264.7	Mus musculus	IC50	>	50000.0	nM	PMID[35608269]
NPT21742	Cell line	L02	Homo sapiens	IC50	>	50000.0	nM	PMID[35608269]

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 NPC608769 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	18997
0.1-0.2	29980
0.2-0.3	801
0.3-0.4	33
0.4-0.5	10
0.5-0.6	9
0.6-0.7	18
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC100390
1.0	High Similarity	NPC254614
1.0	High Similarity	NPC600930
0.8554	High Similarity	NPC604937
0.7558	Intermediate Similarity	NPC603774
0.7416	Intermediate Similarity	NPC79835
0.7416	Intermediate Similarity	NPC603465
0.7222	Intermediate Similarity	NPC603368
0.7222	Intermediate Similarity	NPC610240
0.7	Intermediate Similarity	NPC243014
0.6889	Remote Similarity	NPC264192
0.6842	Remote Similarity	NPC601164
0.6813	Remote Similarity	NPC254146
0.6813	Remote Similarity	NPC33378
0.6813	Remote Similarity	NPC6274
0.6813	Remote Similarity	NPC486573
0.6813	Remote Similarity	NPC606278
0.6739	Remote Similarity	NPC600931
0.6566	Remote Similarity	NPC600933
0.6566	Remote Similarity	NPC601161
0.6413	Remote Similarity	NPC188291
0.6413	Remote Similarity	NPC15215
0.6413	Remote Similarity	NPC242486
0.6344	Remote Similarity	NPC600158
0.6344	Remote Similarity	NPC609951
0.6304	Remote Similarity	NPC484693
0.6129	Remote Similarity	NPC605817
0.6019	Remote Similarity	NPC602548
0.5876	Remote Similarity	NPC484694
0.5876	Remote Similarity	NPC600403
0.5806	Remote Similarity	NPC607087
0.5534	Remote Similarity	NPC606873
0.5464	Remote Similarity	NPC610580
0.5204	Remote Similarity	NPC607711
0.5155	Remote Similarity	NPC610579
0.51	Remote Similarity	NPC601160
0.51	Remote Similarity	NPC605654

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608769 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6617
0.1-0.2	2499
0.2-0.3	34
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