NPASS Compound

Natural Product: NPC38513

Natural Product ID	NPC38513
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Deca-1,9-Diene
IUPAC Name	deca-1,9-diene
Synonyms	Deca-1,9-Diene
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL31020
PubChem CID	15439
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002837] Hydrocarbons [CHEMONTID:0004475] Unsaturated hydrocarbons [CHEMONTID:0002838] Olefins [CHEMONTID:0002839] Acyclic olefins [CHEMONTID:0001019] Alkadienes

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 28 27 0 0 0 0 0 0 0 0999 V2000 -2.5944 1.8799 0.8312 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3048 0.8242 0.0550 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6819 -0.5226 0.4982 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6128 -1.5068 0.7598 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7161 -1.9598 -0.3063 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1514 -0.9810 -1.0137 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0498 -0.2659 -0.0253 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9319 0.7330 -0.7656 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8009 1.4187 0.2259 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1230 1.3635 0.1719 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3104 2.8582 0.4901 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0986 1.7646 1.7751 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8158 1.0462 -0.8733 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4894 -0.9296 -0.1784 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2406 -0.4129 1.4877 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1575 -2.4413 1.1429 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0681 -1.1485 1.6802 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0013 -2.7507 0.1056 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2975 -2.5830 -1.0676 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9019 -1.6544 -1.5906 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3145 -0.3319 -1.7531 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4934 0.2724 0.7459 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6986 -1.0154 0.4575 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3322 1.5121 -1.2621 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5781 0.1708 -1.4856 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3238 1.9907 1.0307 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7303 1.8711 0.9052 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5855 0.7983 -0.6236 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 7 8 1 0 8 9 1 0 9 10 2 0 1 11 1 0 1 12 1 0 2 13 1 0 3 14 1 0 3 15 1 0 4 16 1 0 4 17 1 0 5 18 1 0 5 19 1 0 6 20 1 0 6 21 1 0 7 22 1 0 7 23 1 0 8 24 1 0 8 25 1 0 9 26 1 0 10 27 1 0 10 28 1 0 M END

Standard InCHIKey	NLDGJRWPPOSWLC-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H18/c1-3-5-7-9-10-8-6-4-2/h3-4H,1-2,5-10H2
SMILES	C=CCCCCCCC=C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	138.14	Volume:	176.243 ? Van der Waals volume.
Dense:	0.784	LogP:	4.783 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.327 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.838 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	2.0
TPSA:	0.0 ? Topological Polar Surface Area.	H-Bond Acceptor:	0.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	0.0

MedChem Properties

QED Drug-Likeness Score:	0.371	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.277	Fsp³:	0.6
MCE-18:	0.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.041	Fluc inhibitor:	0.376 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.006 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	1.0	Promiscuous compounds:	0.108

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.844	MDCK Permeability:	-4.688
Pgp-inhibitor:	0.868	Pgp-substrate:	0.0
PAMPA:	0.002 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.049
20% Bioavailability (F20%):	0.567	30% Bioavailability (F30%):	0.872
50% Bioavailability (F50%):	0.847

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.639	MRP1:	0.673
Plasma Protein Binding (PPB):	97.434%	Volume Distribution (VD):	0.351
Fu:	2.734% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.951
OATP1B3 inhibitor:	0.959	BCRP inhibitor:	0.978
BSEP inhibitor:	0.588

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.005	CYP2C19-substrate:	0.028
CYP2C9-inhibitor:	0.998	CYP2C9-substrate:	0.36
CYP2D6-inhibitor:	0.986	CYP2D6-substrate:	0.986
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.173	CYP2C8-inhibitor:	1.0
HLM stability:	0.397 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

6.965

Half-life (T1/2):

0.552

ADMET: Toxicity

hERG Blockers:	0.082	hERG Blockers (10um):	0.687
Human Hepatotoxicity (H-HT):	0.142	Drug-induced Liver Injury (DILI):	0.045
AMES Toxicity:	0.393	Rat Oral Acute Toxicity:	0.37
Maximum Recommended Daily Dose:	0.258	Skin Sensitization:	0.996
Carcinogencity:	0.53	Eye Corrosion:	0.999
Eye Irritation:	0.999	Respiratory Toxicity:	0.593
Drug-induced Neurotoxicity:	0.456	Ototoxicity:	0.105
Hematotoxicity:	0.081	Drug-induced Nephrotoxicity:	0.028
Genotoxicity:	0.009	RPMI-8226 Immunitoxicity:	0.037
A549 Cytotoxicity:	0.175	Hek293 Cytotoxicity:	0.044
BCF:	2.984 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.766 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.525 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.724 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7642	Cleome gynandra	Species	Cleomaceae	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
Potency	27
MES	1

Activity Type	# Activity
Individual protein	6
Organism	1
Others	21

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT153	Individual protein	Androgen Receptor	Homo sapiens	Potency	n.a.	61795.7	nM	PubChem BioAssay data set
NPT106	Individual protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	Potency	n.a.	61795.7	nM	PubChem BioAssay data set
NPT162	Individual protein	Heat shock protein beta-1	Homo sapiens	Potency	n.a.	55075.5	nM	PubChem BioAssay data set
NPT106	Individual protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	Potency	n.a.	55075.5	nM	PubChem BioAssay data set
NPT163	Individual protein	Nuclear factor NF-kappa-B p105 subunit	Homo sapiens	Potency	n.a.	55075.5	nM	PubChem BioAssay data set
NPT152	Individual protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	13.3	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT419	Organism	Oryctolagus cuniculus	Oryctolagus cuniculus	MES	=	0.37	n.a.	PMID[12672239]
NPT2	Others	Unspecified	n.a.	Potency	n.a.	55075.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	5507.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	61795.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	68729.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	49086.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	12222	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	87288.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	24601.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	38649.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	54593.5	nM	PubChem BioAssay data set

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 NPC38513 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	46318
0.1-0.2	3135
0.2-0.3	321
0.3-0.4	61
0.4-0.5	14
0.5-0.6	2
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	Natural Product ID
0.7692	Intermediate Similarity	NPC266539
0.7692	Intermediate Similarity	NPC179103
0.7692	Intermediate Similarity	NPC88325
0.7692	Intermediate Similarity	NPC287191
0.7692	Intermediate Similarity	NPC31891
0.7692	Intermediate Similarity	NPC266144
0.7692	Intermediate Similarity	NPC76765
0.5882	Remote Similarity	NPC16561
0.5385	Remote Similarity	NPC178306

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC38513 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8876
0.1-0.2	256
0.2-0.3	17
0.3-0.4	0
0.4-0.5	1
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