NPASS Compound

Natural Product: NPC175334

Natural Product ID	NPC175334
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OPTVCEJJRRFTRJ-PSMDKKMZSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11995070
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

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 51 52 0 0 0 0 0 0 0 0999 V2000 0.6743 3.4737 0.7136 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2433 2.3580 0.1830 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5321 2.3872 -1.0798 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7463 1.5100 -1.0281 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6444 0.4299 0.0410 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6881 -0.5891 -0.1650 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7372 -0.4636 0.9345 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5065 -0.3392 -1.4469 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2543 -2.0215 -0.1702 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0179 -2.3362 0.5665 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3380 -1.1912 1.2281 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2268 -0.0565 0.2249 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4198 -0.5736 -1.0108 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5217 1.0755 0.8468 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9725 0.8334 1.1616 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8937 0.8144 0.0677 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7114 -0.1547 -0.2216 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6230 -0.0450 -1.3961 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6495 0.9542 -2.1434 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7814 -1.3656 0.5615 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4771 -2.4887 -0.2614 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4972 4.4636 0.2751 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2301 3.4615 1.6303 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0624 2.1708 -1.9887 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8898 3.4459 -1.2592 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8886 1.0846 -2.0428 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6397 2.1480 -0.8570 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8420 0.9603 0.9970 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2774 -1.4420 1.0832 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2341 -0.1952 1.8857 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4734 0.3356 0.7140 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4038 -1.0189 -1.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9795 -0.6581 -2.3373 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9121 0.6784 -1.4746 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1394 -2.3655 -1.2210 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0703 -2.6927 0.2393 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1951 -3.0937 1.3931 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2682 -2.8732 -0.0760 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6405 -1.5433 1.5913 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9126 -0.7875 2.0921 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0198 -1.4675 -0.7436 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3024 -0.9370 -1.7745 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1426 0.1149 -1.4961 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0433 1.1897 1.8830 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2509 1.7731 1.7656 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0133 0.0639 1.9349 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8993 1.7176 -0.5851 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2715 -0.8655 -1.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0130 -1.4062 1.3424 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7919 -1.6201 0.9469 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2767 -2.8530 -0.6766 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 2 0 17 20 1 0 20 21 1 0 14 2 1 0 12 5 1 0 1 22 1 0 1 23 1 0 3 24 1 0 3 25 1 0 4 26 1 0 4 27 1 0 5 28 1 1 7 29 1 0 7 30 1 0 7 31 1 0 8 32 1 0 8 33 1 0 8 34 1 0 9 35 1 0 9 36 1 0 10 37 1 0 10 38 1 0 11 39 1 0 11 40 1 0 13 41 1 0 13 42 1 0 13 43 1 0 14 44 1 1 15 45 1 0 15 46 1 0 16 47 1 0 18 48 1 0 20 49 1 0 20 50 1 0 21 51 1 0 M END

Standard InCHIKey	OPTVCEJJRRFTRJ-PSMDKKMZSA-N
Standard InCHI	InChI=1S/C19H30O2/c1-14-6-9-17-18(2,3)10-5-11-19(17,4)16(14)8-7-15(12-20)13-21/h7,12,16-17,21H,1,5-6,8-11,13H2,2-4H3/b15-7-/t16-,17-,19+/m0/s1
SMILES	C=C1CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1C/C=C(/C=O)CO

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	2
Inhibition	1

Activity Type	# Activity
Cell line	1
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
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	28700.0	nM	PMID[31710213]
NPT2	Others	Unspecified	n.a.	Inhibition	=	27.1	%	PMID[31710213]
NPT2	Others	Unspecified	n.a.	IC50	>	50000.0	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 NPC175334 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	19990
0.1-0.2	24940
0.2-0.3	4336
0.3-0.4	461
0.4-0.5	86
0.5-0.6	29
0.6-0.7	10
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
0.7872	Intermediate Similarity	NPC99321
0.7234	Intermediate Similarity	NPC169275
0.7234	Intermediate Similarity	NPC52449
0.7083	Intermediate Similarity	NPC189745
0.6667	Remote Similarity	NPC144947
0.6538	Remote Similarity	NPC217394
0.6538	Remote Similarity	NPC238146
0.6415	Remote Similarity	NPC79027
0.6415	Remote Similarity	NPC75485
0.6415	Remote Similarity	NPC168975
0.64	Remote Similarity	NPC484731
0.6275	Remote Similarity	NPC478390
0.6122	Remote Similarity	NPC68703
0.6038	Remote Similarity	NPC12170
0.5918	Remote Similarity	NPC149680
0.5918	Remote Similarity	NPC226997
0.5918	Remote Similarity	NPC600344
0.58	Remote Similarity	NPC268039
0.5741	Remote Similarity	NPC251528
0.5714	Remote Similarity	NPC469
0.5714	Remote Similarity	NPC478393
0.5714	Remote Similarity	NPC41160
0.5714	Remote Similarity	NPC67840
0.566	Remote Similarity	NPC476949
0.5577	Remote Similarity	NPC470428
0.5577	Remote Similarity	NPC484730
0.5577	Remote Similarity	NPC484729
0.5517	Remote Similarity	NPC478394
0.5517	Remote Similarity	NPC255174
0.5439	Remote Similarity	NPC472809
0.5439	Remote Similarity	NPC472810
0.5439	Remote Similarity	NPC475709
0.5424	Remote Similarity	NPC489287
0.5283	Remote Similarity	NPC185587
0.5185	Remote Similarity	NPC35655
0.5172	Remote Similarity	NPC311070
0.5172	Remote Similarity	NPC177037
0.5172	Remote Similarity	NPC472814
0.5167	Remote Similarity	NPC489288
0.5161	Remote Similarity	NPC131366
0.5098	Remote Similarity	NPC481631
0.5085	Remote Similarity	NPC253186
0.5079	Remote Similarity	NPC87335

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC175334 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7001
0.1-0.2	2052
0.2-0.3	89
0.3-0.4	6
0.4-0.5	1
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
0.5172	Remote Similarity	NPD4695	Discontinued

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