NPASS Compound

Natural Product: NPC66124

Natural Product ID	NPC66124
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Nonanol
IUPAC Name	nonan-3-ol
Synonyms	3-Nonanol
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL487999
PubChem CID	12216
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols

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 30 29 0 0 0 0 0 0 0 0999 V2000 -3.9736 0.8739 1.2274 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8245 -0.0003 0.7950 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8315 0.7374 -0.0645 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7335 -0.2452 -0.4298 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3179 0.3841 -1.2906 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3987 -0.5751 -1.6463 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2241 -1.1457 -0.5653 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0436 -0.2374 0.2654 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3897 0.8240 1.0503 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4745 -2.0369 0.2196 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6069 1.9268 1.2196 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3374 0.6307 2.2549 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7900 0.7180 0.4826 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1374 -0.9294 0.2992 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3030 -0.3175 1.7407 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3505 1.1207 -0.9650 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4030 1.6051 0.4656 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2492 -1.0381 -1.0378 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3711 -0.7056 0.4914 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1386 0.7386 -2.2674 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7564 1.2961 -0.8443 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8727 -1.4177 -2.2075 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0582 -0.1390 -2.4574 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9814 -1.8432 -1.0736 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8658 0.2073 -0.3638 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6286 -0.9011 0.9728 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3578 0.5868 1.3569 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9474 0.8885 2.0493 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5060 1.8426 0.6054 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2273 -2.8485 -0.2828 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 1 0 8 9 1 0 7 10 1 0 1 11 1 0 1 12 1 0 1 13 1 0 2 14 1 0 2 15 1 0 3 16 1 0 3 17 1 0 4 18 1 0 4 19 1 0 5 20 1 0 5 21 1 0 6 22 1 0 6 23 1 0 7 24 1 0 8 25 1 0 8 26 1 0 9 27 1 0 9 28 1 0 9 29 1 0 10 30 1 0 M END

Standard InCHIKey	GYSCXPVAKHVAAY-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C9H20O/c1-3-5-6-7-8-9(10)4-2/h9-10H,3-8H2,1-2H3
SMILES	CCCCCCC(CC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	144.15	Volume:	173.011 ? Van der Waals volume.
Dense:	0.833	LogP:	3.03 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.62 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.479 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	0.0
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:	0.568	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.317	Fsp³:	1.0
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:	0.071	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.999	Promiscuous compounds:	0.089

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.988	MDCK Permeability:	-4.72
Pgp-inhibitor:	0.063	Pgp-substrate:	0.699
PAMPA:	0.224 ? 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):	0.744
20% Bioavailability (F20%):	0.514	30% Bioavailability (F30%):	0.838
50% Bioavailability (F50%):	0.526

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.869	MRP1:	0.863
Plasma Protein Binding (PPB):	88.003%	Volume Distribution (VD):	0.157
Fu:	15.02% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.061
OATP1B3 inhibitor:	0.668	BCRP inhibitor:	0.725
BSEP inhibitor:	0.291

ADMET: Metabolism

CYP1A2-inhibitor:	0.015	CYP1A2-substrate:	0.914
CYP2C19-inhibitor:	0.72	CYP2C19-substrate:	0.22
CYP2C9-inhibitor:	0.814	CYP2C9-substrate:	0.45
CYP2D6-inhibitor:	0.78	CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.008	CYP3A4-substrate:	0.863
CYP2B6-substrate:	0.897	CYP2C8-inhibitor:	0.792
HLM stability:	0.154 ? 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):

9.785

Half-life (T1/2):

1.0

ADMET: Toxicity

hERG Blockers:	0.182	hERG Blockers (10um):	0.677
Human Hepatotoxicity (H-HT):	0.42	Drug-induced Liver Injury (DILI):	0.06
AMES Toxicity:	0.146	Rat Oral Acute Toxicity:	0.12
Maximum Recommended Daily Dose:	0.189	Skin Sensitization:	0.871
Carcinogencity:	0.295	Eye Corrosion:	0.994
Eye Irritation:	0.998	Respiratory Toxicity:	0.808
Drug-induced Neurotoxicity:	0.12	Ototoxicity:	0.353
Hematotoxicity:	0.183	Drug-induced Nephrotoxicity:	0.263
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.047
A549 Cytotoxicity:	0.302	Hek293 Cytotoxicity:	0.094
BCF:	1.185 ? 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:	3.402 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.502 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.999 ? 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
NPO60587	Hypericum revolutum subsp. keniense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36636606]
NPO52966	Clinopodium nepeta subsp. spruneri	Genus	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38140425]
NPO23256	Mentha arvensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13857	Mentha canadensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23256	Mentha arvensis	Species	Lamiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO23256	Mentha arvensis	Species	Lamiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO13857	Mentha canadensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13857	Mentha canadensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23256	Mentha arvensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23256	Mentha arvensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13857	Mentha canadensis	Species	Lamiaceae	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
NPO52966	Clinopodium nepeta subsp. spruneri	Oil	n.a.	0.2	n.a.	n.a.	%	PMID[38140425]
NPO52966	Clinopodium nepeta subsp. spruneri	Oil	n.a.	0.6	n.a.	n.a.	%	PMID[38140425]
NPO52966	Clinopodium nepeta subsp. spruneri	Oil	n.a.	0.3	n.a.	n.a.	%	PMID[38140425]
NPO52966	Clinopodium nepeta subsp. spruneri	Oil	n.a.	0.4	n.a.	n.a.	%	PMID[38140425]
NPO60587	Hypericum revolutum subsp. keniense	Oil	Leaves	0	n.a.	n.a.	%	PMID[36636606]
NPO60587	Hypericum revolutum subsp. keniense	Oil	Flowers	0.1	n.a.	n.a.	%	PMID[36636606]

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
MIC	1

Activity Type	# Activity
Organism	1

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
NPT167	Organism	Propionibacterium acnes	Propionibacterium acnes	MIC	=	200.0	ug.mL-1	PMID[8158169]

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 NPC66124 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	35405
0.1-0.2	13097
0.2-0.3	1043
0.3-0.4	233
0.4-0.5	55
0.5-0.6	8
0.6-0.7	10
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9375	High Similarity	NPC122962
0.7647	Intermediate Similarity	NPC159845
0.6667	Remote Similarity	NPC319034
0.6667	Remote Similarity	NPC1748
0.6667	Remote Similarity	NPC72324
0.6667	Remote Similarity	NPC97967
0.6667	Remote Similarity	NPC193062
0.6471	Remote Similarity	NPC608484
0.6364	Remote Similarity	NPC474392
0.625	Remote Similarity	NPC325345
0.6111	Remote Similarity	NPC110884
0.6087	Remote Similarity	NPC479534
0.5882	Remote Similarity	NPC232554
0.5652	Remote Similarity	NPC474914
0.5625	Remote Similarity	NPC252154
0.5217	Remote Similarity	NPC478319
0.5217	Remote Similarity	NPC121062
0.5217	Remote Similarity	NPC29222
0.5217	Remote Similarity	NPC96966
0.5217	Remote Similarity	NPC602997

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC66124 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7946
0.1-0.2	1129
0.2-0.3	66
0.3-0.4	3
0.4-0.5	4
0.5-0.6	1
0.6-0.7	1
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
0.625	Remote Similarity	NPD8988	Clinical (unspecified phase)
0.5217	Remote Similarity	NPD3214	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