NPASS Compound

Natural Product: NPC12170

Natural Product ID	NPC12170
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GFLZVIUGJVSYJX-OFWUXJPWSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10881199
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

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 52 54 0 0 0 0 0 0 0 0999 V2000 0.5647 2.8208 1.2040 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2571 1.9787 0.2170 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5189 2.3630 -0.9801 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7172 1.4453 -1.1316 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7501 0.5598 0.1043 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0405 -0.1344 0.2554 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8565 -0.2151 -1.0456 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8959 0.8530 1.1096 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0872 -1.4693 0.8715 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8273 -2.0547 1.3788 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6503 -1.1551 1.3729 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4960 -0.3244 0.1165 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4979 -1.2373 -1.0683 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7130 0.5349 0.2954 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8061 0.4002 -0.6983 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4703 -0.9094 -0.7838 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7946 -0.9717 -0.5447 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6066 0.2011 -0.2039 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9853 -0.3685 0.0424 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9730 -1.6778 -0.4854 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6618 -2.1189 -0.5651 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3160 -3.3227 -0.6415 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2638 3.8483 1.1921 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1374 2.4563 2.0466 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1124 2.3866 -1.9016 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8624 3.4316 -0.8640 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5523 0.8790 -2.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6461 2.0102 -1.1799 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5905 1.2500 0.9585 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4270 0.3181 -1.8795 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8946 0.1736 -0.9066 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0296 -1.3109 -1.2761 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1987 1.7104 0.4767 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2866 1.1715 1.9813 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8167 0.3176 1.3876 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5580 -2.2393 0.1850 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8207 -1.4460 1.7238 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9371 -2.4468 2.4263 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5304 -2.9744 0.7900 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7447 -0.4120 2.2197 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3032 -1.7017 1.5193 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2555 -2.2682 -0.7540 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5958 -1.3350 -1.3890 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0897 -0.9227 -1.9259 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1592 0.3574 1.3164 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5727 1.2311 -0.5935 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4212 0.5935 -1.7525 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0100 -1.8419 -1.0200 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6118 0.9783 -0.9920 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2417 0.6064 0.7605 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7800 0.2742 -0.4205 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2330 -0.4479 1.1210 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 6 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 6 12 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 14 2 1 0 21 17 1 0 12 5 1 0 1 23 1 0 1 24 1 0 3 25 1 0 3 26 1 0 4 27 1 0 4 28 1 0 5 29 1 1 7 30 1 0 7 31 1 0 7 32 1 0 8 33 1 0 8 34 1 0 8 35 1 0 9 36 1 0 9 37 1 0 10 38 1 0 10 39 1 0 11 40 1 0 11 41 1 0 13 42 1 0 13 43 1 0 13 44 1 0 14 45 1 1 15 46 1 0 15 47 1 0 16 48 1 0 18 49 1 0 18 50 1 0 19 51 1 0 19 52 1 0 M END

Standard InCHIKey	GFLZVIUGJVSYJX-OFWUXJPWSA-N
Standard InCHI	InChI=1S/C20H30O2/c1-14-6-9-17-19(2,3)11-5-12-20(17,4)16(14)8-7-15-10-13-22-18(15)21/h7,16-17H,1,5-6,8-13H2,2-4H3/b15-7+/t16-,17-,20+/m0/s1
SMILES	C=C1CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1C/C=C/1CCOC1=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
NPO41076	Amomum villosum	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[31710213]
NPO41076	Amomum villosum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	9
Inhibition	1
Activity	12

Activity Type	# Activity
Cell line	20
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
NPT146	Cell line	SK-OV-3	Homo sapiens	IC50	=	2.0	ug.mL-1	PMID[16384699]
NPT737	Cell line	HUVEC	Homo sapiens	IC50	=	1.7	ug.mL-1	PMID[16384699]
NPT737	Cell line	HUVEC	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[16384699]
NPT933	Cell line	U373 MG	Homo sapiens	IC50	=	15.1	ug.mL-1	PMID[16384699]
NPT319	Cell line	B16	Mus musculus	IC50	=	17.6	ug.mL-1	PMID[16384699]
NPT1535	Cell line	U-87 MG	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[16384699]
NPT2245	Cell line	SiHa	Homo sapiens	IC50	=	20.2	ug.mL-1	PMID[16384699]
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	30800.0	nM	PMID[31710213]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	103.0	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	107.3	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	102.4	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	100.0	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	104.4	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	94.6	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	73.1	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	52.6	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	93.9	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	83.9	%	PMID[31022551]
NPT113	Cell line	RAW264.7	Mus musculus	Activity	=	76.3	%	PMID[31022551]
NPT2	Others	Unspecified	n.a.	Inhibition	=	89.1	%	PMID[31710213]
NPT2	Others	Unspecified	n.a.	IC50	=	17100.0	nM	PMID[31710213]

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 NPC12170 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	20114
0.1-0.2	25003
0.2-0.3	4205
0.3-0.4	428
0.4-0.5	65
0.5-0.6	23
0.6-0.7	15
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
0.7551	Intermediate Similarity	NPC478390
0.7115	Intermediate Similarity	NPC217394
0.6981	Remote Similarity	NPC79027
0.6909	Remote Similarity	NPC478394
0.6852	Remote Similarity	NPC469
0.6852	Remote Similarity	NPC478393
0.6852	Remote Similarity	NPC478375
0.6667	Remote Similarity	NPC50488
0.6667	Remote Similarity	NPC474396
0.6491	Remote Similarity	NPC72845
0.6296	Remote Similarity	NPC144947
0.6154	Remote Similarity	NPC169275
0.6154	Remote Similarity	NPC52449
0.6111	Remote Similarity	NPC99321
0.6038	Remote Similarity	NPC175334
0.6038	Remote Similarity	NPC35655
0.6	Remote Similarity	NPC251528
0.5965	Remote Similarity	NPC177037
0.5965	Remote Similarity	NPC478369
0.5965	Remote Similarity	NPC472814
0.5893	Remote Similarity	NPC238146
0.569	Remote Similarity	NPC311070
0.569	Remote Similarity	NPC475709
0.5667	Remote Similarity	NPC478391
0.5556	Remote Similarity	NPC185587
0.5517	Remote Similarity	NPC75485
0.5517	Remote Similarity	NPC168975
0.5455	Remote Similarity	NPC189745
0.5424	Remote Similarity	NPC472809
0.5424	Remote Similarity	NPC472810
0.5357	Remote Similarity	NPC4509
0.5185	Remote Similarity	NPC268039
0.5179	Remote Similarity	NPC484731
0.5172	Remote Similarity	NPC471654
0.5172	Remote Similarity	NPC106416
0.5172	Remote Similarity	NPC16321
0.5172	Remote Similarity	NPC86316
0.5172	Remote Similarity	NPC609165
0.5161	Remote Similarity	NPC489288
0.5085	Remote Similarity	NPC200513

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC12170 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6854
0.1-0.2	2180
0.2-0.3	112
0.3-0.4	1
0.4-0.5	2
0.5-0.6	1
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
0.5085	Remote Similarity	NPD4752	Clinical (unspecified phase)

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