NPASS Compound

Natural Product: NPC500992

Natural Product ID	NPC500992
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FKLSONDBCYHMOQ-UHFFFAOYSA-N
IUPAC Name	dodec-9-enoic acid
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

RDKit 3D 36 35 0 0 0 0 0 0 0 0999 V2000 -6.1360 0.4919 0.1147 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7077 1.0033 0.0337 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9098 0.2776 -0.9681 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8198 -0.4149 -0.7707 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1141 -0.6458 0.4958 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6877 -0.1247 0.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1331 -0.7728 -0.5956 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5283 -0.2061 -0.5829 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2092 -0.4352 0.7331 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6262 0.1351 0.7259 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4918 -0.4833 -0.3206 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8399 0.1707 -0.2025 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6642 -0.1242 0.6784 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1742 1.1509 -1.1255 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8483 1.3435 0.1405 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3953 -0.1849 -0.7151 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3003 -0.0611 1.0763 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7597 2.0948 -0.2542 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2841 0.9904 1.0435 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3010 0.3420 -2.0036 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3554 -0.8948 -1.6559 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6324 -0.1176 1.3144 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1038 -1.7397 0.6963 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 -0.4159 1.4530 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7100 0.9555 0.3055 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3034 -0.6382 -1.6210 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2105 -1.8765 -0.4682 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4696 0.9160 -0.7088 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1281 -0.5433 -1.4539 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2513 -1.4830 1.0460 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6605 0.1895 1.5001 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6104 1.2262 0.6264 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0572 -0.1405 1.7176 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6780 -1.5654 -0.1214 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1424 -0.3699 -1.3549 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7392 1.9501 -0.8746 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 3 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 12 14 1 0 1 15 1 0 1 16 1 0 1 17 1 0 2 18 1 0 2 19 1 0 3 20 1 0 4 21 1 0 5 22 1 0 5 23 1 0 6 24 1 0 6 25 1 0 7 26 1 0 7 27 1 0 8 28 1 0 8 29 1 0 9 30 1 0 9 31 1 0 10 32 1 0 10 33 1 0 11 34 1 0 11 35 1 0 14 36 1 0 M END

Standard InCHIKey	FKLSONDBCYHMOQ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C12H22O2/c1-2-3-4-5-6-7-8-9-10-11-12(13)14/h3-4H,2,5-11H2,1H3,(H,13,14)
SMILES	CCC=CCCCCCCCC(=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
NPO59685	Streptomyces sp. mNP10	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO56232	Afzelia cuanzesis	Genus	Fabaceae	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

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

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 NPC500992 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	38604
0.1-0.2	9664
0.2-0.3	1212
0.3-0.4	200
0.4-0.5	68
0.5-0.6	33
0.6-0.7	38
0.7-0.8	1
0.8-0.85	0
0.85-0.9	15
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8966	High Similarity	NPC52955
0.8966	High Similarity	NPC88966
0.8966	High Similarity	NPC25417
0.8966	High Similarity	NPC1813
0.8889	High Similarity	NPC281245
0.8621	High Similarity	NPC70387
0.8571	High Similarity	NPC424
0.8571	High Similarity	NPC36061
0.8571	High Similarity	NPC69510
0.8571	High Similarity	NPC77272
0.8571	High Similarity	NPC290563
0.8571	High Similarity	NPC139029
0.8571	High Similarity	NPC281972
0.8571	High Similarity	NPC261831
0.8571	High Similarity	NPC87564
0.7931	Intermediate Similarity	NPC92114
0.7742	Intermediate Similarity	NPC154245
0.7742	Intermediate Similarity	NPC85813
0.7742	Intermediate Similarity	NPC223697
0.7742	Intermediate Similarity	NPC6095
0.7667	Intermediate Similarity	NPC149821
0.7667	Intermediate Similarity	NPC95145
0.7667	Intermediate Similarity	NPC325642
0.7667	Intermediate Similarity	NPC65174
0.7419	Intermediate Similarity	NPC321062
0.6897	Remote Similarity	NPC180534
0.6897	Remote Similarity	NPC611531
0.6875	Remote Similarity	NPC5413
0.6857	Remote Similarity	NPC606120
0.6667	Remote Similarity	NPC59051
0.6538	Remote Similarity	NPC214610
0.6538	Remote Similarity	NPC118968
0.6538	Remote Similarity	NPC183424
0.6538	Remote Similarity	NPC294085
0.6486	Remote Similarity	NPC477201
0.6452	Remote Similarity	NPC34416
0.6452	Remote Similarity	NPC117572
0.6429	Remote Similarity	NPC171736
0.6429	Remote Similarity	NPC301585
0.6429	Remote Similarity	NPC261080
0.6429	Remote Similarity	NPC132565
0.6429	Remote Similarity	NPC209970
0.6429	Remote Similarity	NPC216630
0.6429	Remote Similarity	NPC201844
0.6429	Remote Similarity	NPC301696
0.6429	Remote Similarity	NPC196924
0.6429	Remote Similarity	NPC307783
0.6429	Remote Similarity	NPC154186
0.6429	Remote Similarity	NPC149184
0.6429	Remote Similarity	NPC279026
0.6429	Remote Similarity	NPC113928
0.6429	Remote Similarity	NPC14227
0.6389	Remote Similarity	NPC225929
0.6364	Remote Similarity	NPC91495
0.6154	Remote Similarity	NPC243532
0.6154	Remote Similarity	NPC268826
0.6071	Remote Similarity	NPC155263
0.6061	Remote Similarity	NPC207292
0.6053	Remote Similarity	NPC106851
0.6053	Remote Similarity	NPC282788
0.6053	Remote Similarity	NPC274927
0.6	Remote Similarity	NPC68343
0.6	Remote Similarity	NPC328089
0.5897	Remote Similarity	NPC179764
0.5882	Remote Similarity	NPC48162
0.5806	Remote Similarity	NPC55023
0.5806	Remote Similarity	NPC21844
0.575	Remote Similarity	NPC251042
0.575	Remote Similarity	NPC255863
0.575	Remote Similarity	NPC473863
0.575	Remote Similarity	NPC174447
0.575	Remote Similarity	NPC136164
0.575	Remote Similarity	NPC122521
0.575	Remote Similarity	NPC245947
0.5714	Remote Similarity	NPC175342
0.5714	Remote Similarity	NPC174560
0.5714	Remote Similarity	NPC125312
0.5667	Remote Similarity	NPC604140
0.561	Remote Similarity	NPC318420
0.561	Remote Similarity	NPC326268
0.5556	Remote Similarity	NPC134782
0.5526	Remote Similarity	NPC487561
0.5455	Remote Similarity	NPC314679
0.5429	Remote Similarity	NPC294548
0.5366	Remote Similarity	NPC187777
0.5349	Remote Similarity	NPC26500
0.5294	Remote Similarity	NPC8219
0.5185	Remote Similarity	NPC174368
0.5152	Remote Similarity	NPC50457
0.5152	Remote Similarity	NPC604910
0.5143	Remote Similarity	NPC18712
0.5143	Remote Similarity	NPC74845
0.5128	Remote Similarity	NPC284212
0.5122	Remote Similarity	NPC274290
0.5116	Remote Similarity	NPC320642
0.5116	Remote Similarity	NPC329550

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC500992 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6763
0.1-0.2	2110
0.2-0.3	214
0.3-0.4	40
0.4-0.5	6
0.5-0.6	0
0.6-0.7	9
0.7-0.8	1
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8966	High Similarity	NPD3172	Approved
0.8571	High Similarity	NPD3195	Phase 2
0.8571	High Similarity	NPD3196	Approved
0.7742	Intermediate Similarity	NPD4266	Phase 2
0.6897	Remote Similarity	NPD622	Pre-clinical
0.6875	Remote Similarity	NPD3173	Phase 4
0.6857	Remote Similarity	NPD3194	Phase 4
0.6842	Remote Similarity	NPD39	Phase 4
0.6538	Remote Similarity	NPD9655	Phase 4
0.6452	Remote Similarity	NPD4222	Phase 3
0.6429	Remote Similarity	NPD2270	Pre-clinical
0.6429	Remote Similarity	NPD633	Phase 3
0.6429	Remote Similarity	NPD9448	Phase 2

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