NPASS Compound

Natural Product: NPC510086

Natural Product ID	NPC510086
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	dec-3-en-2-ol
IUPAC Name	dec-3-en-2-ol
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 31 30 0 0 0 0 0 0 0 0999 V2000 4.6912 0.6782 -0.4588 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9600 -0.6442 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4955 -0.5050 -0.6794 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8718 0.5176 0.2468 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4151 0.7300 -0.0362 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3922 -0.5451 0.1230 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8014 -0.2117 -0.1797 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7655 -0.3749 0.7117 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1729 -0.0532 0.4409 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6850 -0.6090 -0.8658 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4043 1.3209 0.4401 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1382 1.3878 -1.1108 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7954 1.1942 0.5234 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7229 0.5150 -0.8425 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0920 -0.9562 0.7464 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4744 -1.3892 -0.9451 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4512 -0.1161 -1.7135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0235 -1.4861 -0.5429 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3900 1.4785 0.0472 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0727 0.2598 1.3075 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0407 1.5267 0.6042 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3260 1.0742 -1.0854 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0647 -1.2808 -0.6504 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2487 -1.0193 1.0937 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0470 0.1745 -1.1529 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5026 -0.7633 1.6869 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8080 -0.4914 1.2354 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5747 -0.0132 -1.1982 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0570 -1.6537 -0.7560 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8914 -0.5594 -1.6083 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5452 1.8143 0.3677 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 3 8 9 1 0 9 10 1 0 9 11 1 0 1 12 1 0 1 13 1 0 1 14 1 0 2 15 1 0 2 16 1 0 3 17 1 0 3 18 1 0 4 19 1 0 4 20 1 0 5 21 1 0 5 22 1 0 6 23 1 0 6 24 1 0 7 25 1 0 8 26 1 0 9 27 1 0 10 28 1 0 10 29 1 0 10 30 1 0 11 31 1 0 M END

Standard InCHIKey	HZRSDQXGMJFUKO-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C10H20O/c1-3-4-5-6-7-8-9-10(2)11/h8-11H,3-7H2,1-2H3
SMILES	CCCCCCC=CC(C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	156.15	Volume:	187.67 ? Van der Waals volume.
Dense:	0.832	LogP:	3.287 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.772 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.731 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	1.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	0.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.463	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.739	Fsp³:	0.8
MCE-18:	1.0 ? 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:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.02	Fluc inhibitor:	0.0 ? 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:	0.004 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.998	Promiscuous compounds:	0.368

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.712	MDCK Permeability:	-4.689
Pgp-inhibitor:	0.033	Pgp-substrate:	0.218
PAMPA:	0.095 ? 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):	0.31
20% Bioavailability (F20%):	0.201	30% Bioavailability (F30%):	0.665
50% Bioavailability (F50%):	0.672

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.712	MRP1:	0.728
Plasma Protein Binding (PPB):	94.614%	Volume Distribution (VD):	0.298
Fu:	7.411% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.303
OATP1B3 inhibitor:	0.963	BCRP inhibitor:	0.435
BSEP inhibitor:	0.378

ADMET: Metabolism

CYP1A2-inhibitor:	0.006	CYP1A2-substrate:	0.986
CYP2C19-inhibitor:	0.862	CYP2C19-substrate:	0.338
CYP2C9-inhibitor:	0.998	CYP2C9-substrate:	0.21
CYP2D6-inhibitor:	0.95	CYP2D6-substrate:	0.861
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.994	CYP2C8-inhibitor:	0.999
HLM stability:	0.699 ? 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):

6.794

Half-life (T1/2):

0.932

ADMET: Toxicity

hERG Blockers:	0.277	hERG Blockers (10um):	0.723
Human Hepatotoxicity (H-HT):	0.203	Drug-induced Liver Injury (DILI):	0.013
AMES Toxicity:	0.177	Rat Oral Acute Toxicity:	0.185
Maximum Recommended Daily Dose:	0.046	Skin Sensitization:	0.943
Carcinogencity:	0.101	Eye Corrosion:	0.998
Eye Irritation:	0.998	Respiratory Toxicity:	0.619
Drug-induced Neurotoxicity:	0.086	Ototoxicity:	0.466
Hematotoxicity:	0.086	Drug-induced Nephrotoxicity:	0.207
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.046
A549 Cytotoxicity:	0.279	Hek293 Cytotoxicity:	0.047
BCF:	1.788 ? 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:	3.996 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.141 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.618 ? 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
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26521454]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22033	Cnidium officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22033	Cnidium officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22033	Cnidium officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18951	Ligusticum sinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22033	Cnidium officinale	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18951	Ligusticum sinense	Species	Apiaceae	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

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 NPC510086 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	32661
0.1-0.2	15290
0.2-0.3	1432
0.3-0.4	352
0.4-0.5	91
0.5-0.6	25
0.6-0.7	4
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
0.68	Remote Similarity	NPC249670
0.6538	Remote Similarity	NPC474642
0.6538	Remote Similarity	NPC473913
0.6	Remote Similarity	NPC151719
0.5862	Remote Similarity	NPC55068
0.5667	Remote Similarity	NPC91226
0.5667	Remote Similarity	NPC243546
0.5667	Remote Similarity	NPC31194
0.5667	Remote Similarity	NPC248884
0.56	Remote Similarity	NPC125122
0.56	Remote Similarity	NPC471276
0.56	Remote Similarity	NPC471280
0.56	Remote Similarity	NPC76976
0.56	Remote Similarity	NPC471281
0.5484	Remote Similarity	NPC72699
0.5484	Remote Similarity	NPC473865
0.5484	Remote Similarity	NPC489234
0.5385	Remote Similarity	NPC170776
0.5385	Remote Similarity	NPC9273
0.5385	Remote Similarity	NPC165447
0.5385	Remote Similarity	NPC471959
0.5385	Remote Similarity	NPC199286
0.5385	Remote Similarity	NPC489046
0.5385	Remote Similarity	NPC76198
0.5385	Remote Similarity	NPC610719
0.52	Remote Similarity	NPC252978
0.5185	Remote Similarity	NPC607242
0.5172	Remote Similarity	NPC600749
0.5172	Remote Similarity	NPC601019

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC510086 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7832
0.1-0.2	1219
0.2-0.3	81
0.3-0.4	15
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
0.5862	Remote Similarity	NPD3210	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