NPASS Compound

Natural Product: NPC63172

Natural Product ID	NPC63172
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	1-Pentacosanol
IUPAC Name	pentacosan-1-ol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	92247
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 78 77 0 0 0 0 0 0 0 0999 V2000 -6.1907 -4.3834 -0.1347 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8742 -3.8099 1.0728 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8790 -2.2932 0.9621 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6031 -1.8262 -0.2628 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5931 -0.3258 -0.3117 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1744 0.2011 -0.3617 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1713 1.7219 -0.4277 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7570 2.2047 -0.4603 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0340 1.6748 -1.6465 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5898 2.1939 -1.7080 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8927 1.7435 -0.4684 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4168 2.1543 -0.4044 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3472 3.6412 -0.4437 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0089 4.1994 -0.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8955 4.0205 0.7482 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3371 2.6878 1.1913 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0609 1.8691 0.1585 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4529 0.5131 0.7681 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1885 -0.3155 -0.2872 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5871 -1.6520 0.2430 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4899 -1.5642 1.4247 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7624 -0.8437 1.1201 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5613 -1.4911 0.0234 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9629 -2.8969 0.3395 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7604 -3.4127 -0.8607 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1334 -4.7127 -0.5721 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9563 -5.4415 0.0785 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8539 -4.3024 -1.0183 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2440 -3.8403 -0.3662 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9299 -4.1275 1.1023 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3159 -4.1188 1.9685 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7931 -2.0083 0.8340 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2253 -1.7969 1.8812 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6354 -2.2260 -0.3345 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9831 -2.1647 -1.1454 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2289 0.0935 -1.0943 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0116 0.0200 0.6787 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7381 -0.1720 -1.3060 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6108 -0.0538 0.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7655 2.1651 0.3956 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6975 1.9857 -1.3687 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2695 1.7986 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7313 3.3080 -0.3820 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4900 1.9074 -2.6080 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8952 0.5626 -1.4990 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5989 3.2929 -1.8743 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1175 1.6756 -2.5820 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3497 2.2922 0.4057 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9726 0.6609 -0.3864 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0849 1.6912 -1.2923 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0348 1.6671 0.4921 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8097 3.9530 -1.4399 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0300 4.0524 0.3469 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8842 5.3362 -0.5333 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4984 3.9331 -1.3860 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3520 4.4772 1.6518 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7871 4.7413 0.6720 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6478 2.1193 1.8313 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1964 2.9264 1.9553 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0127 2.3793 -0.0817 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4075 1.6874 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5593 -0.0647 1.0574 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0750 0.6644 1.6658 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5311 -0.4100 -1.1882 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1026 0.2537 -0.5483 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6220 -2.1851 0.4967 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0617 -2.2027 -0.6106 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9843 -1.0160 2.2526 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6795 -2.5829 1.8565 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5327 0.1943 0.8272 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4134 -0.7585 2.0259 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5053 -0.8991 -0.0939 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0523 -1.4266 -0.9588 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1336 -3.5893 0.4904 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6222 -2.9158 1.2246 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6392 -2.7299 -0.9939 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0997 -3.4083 -1.7519 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1253 -4.6955 -0.3814 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 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 1 27 1 0 1 28 1 0 1 29 1 0 2 30 1 0 2 31 1 0 3 32 1 0 3 33 1 0 4 34 1 0 4 35 1 0 5 36 1 0 5 37 1 0 6 38 1 0 6 39 1 0 7 40 1 0 7 41 1 0 8 42 1 0 8 43 1 0 9 44 1 0 9 45 1 0 10 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 13 52 1 0 13 53 1 0 14 54 1 0 14 55 1 0 15 56 1 0 15 57 1 0 16 58 1 0 16 59 1 0 17 60 1 0 17 61 1 0 18 62 1 0 18 63 1 0 19 64 1 0 19 65 1 0 20 66 1 0 20 67 1 0 21 68 1 0 21 69 1 0 22 70 1 0 22 71 1 0 23 72 1 0 23 73 1 0 24 74 1 0 24 75 1 0 25 76 1 0 25 77 1 0 26 78 1 0 M END

Standard InCHIKey	IACKKVBKKNJZGN-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C25H52O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26/h26H,2-25H2,1H3
SMILES	CCCCCCCCCCCCCCCCCCCCCCCCCO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	368.4	Volume:	449.746 ? Van der Waals volume.
Dense:	0.819	LogP:	8.831 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.626 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-8.274 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	23.0	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:	0.178	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.479	Fsp³:	1.0
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:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.594	Fluc inhibitor:	0.065 ? 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:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.994	Promiscuous compounds:	0.349

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.084	MDCK Permeability:	-4.905
Pgp-inhibitor:	0.001	Pgp-substrate:	0.08
PAMPA:	0.0 ? 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):	0.998
20% Bioavailability (F20%):	0.997	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012	MRP1:	0.986
Plasma Protein Binding (PPB):	101.661%	Volume Distribution (VD):	1.943
Fu:	0.476% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.136
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.991
BSEP inhibitor:	0.368

ADMET: Metabolism

CYP1A2-inhibitor:	0.593	CYP1A2-substrate:	0.444
CYP2C19-inhibitor:	0.444	CYP2C19-substrate:	0.09
CYP2C9-inhibitor:	0.993	CYP2C9-substrate:	0.413
CYP2D6-inhibitor:	0.995	CYP2D6-substrate:	0.305
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	0.999
CYP2B6-substrate:	0.692	CYP2C8-inhibitor:	0.996
HLM stability:	0.281 ? 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):

4.76

Half-life (T1/2):

2.261

ADMET: Toxicity

hERG Blockers:	0.728	hERG Blockers (10um):	0.918
Human Hepatotoxicity (H-HT):	0.525	Drug-induced Liver Injury (DILI):	0.096
AMES Toxicity:	0.018	Rat Oral Acute Toxicity:	0.086
Maximum Recommended Daily Dose:	0.178	Skin Sensitization:	0.996
Carcinogencity:	0.232	Eye Corrosion:	0.988
Eye Irritation:	0.998	Respiratory Toxicity:	0.984
Drug-induced Neurotoxicity:	0.005	Ototoxicity:	0.155
Hematotoxicity:	0.116	Drug-induced Nephrotoxicity:	0.119
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.033
A549 Cytotoxicity:	0.921	Hek293 Cytotoxicity:	0.199
BCF:	0.891 ? 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:	5.259 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.431 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.792 ? 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
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Seeds	Yichun, Heilongjiang Province, China	2018-Sep	PMID[31292343]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO9585	Oenothera biennis	Species	Onagraceae	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
NPO9585	Oenothera biennis	the AOCS method	Seeds	88.75	n.a.	n.a.	mg/kg of oil	PMID[31292343]

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 NPC63172 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	39049
0.1-0.2	9734
0.2-0.3	881
0.3-0.4	126
0.4-0.5	24
0.5-0.6	4
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	15

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC126915
1.0	High Similarity	NPC205141
1.0	High Similarity	NPC24506
1.0	High Similarity	NPC225783
1.0	High Similarity	NPC279895
1.0	High Similarity	NPC185538
1.0	High Similarity	NPC181516
1.0	High Similarity	NPC163556
1.0	High Similarity	NPC139131
1.0	High Similarity	NPC236797
1.0	High Similarity	NPC291158
1.0	High Similarity	NPC272998
1.0	High Similarity	NPC112242
1.0	High Similarity	NPC185041
1.0	High Similarity	NPC147096
0.9286	High Similarity	NPC275462
0.7857	Intermediate Similarity	NPC152759
0.7857	Intermediate Similarity	NPC12231
0.7143	Intermediate Similarity	NPC213764
0.7	Intermediate Similarity	NPC474392
0.7	Intermediate Similarity	NPC76976
0.6667	Remote Similarity	NPC52403
0.65	Remote Similarity	NPC252978
0.6429	Remote Similarity	NPC294703
0.619	Remote Similarity	NPC474914
0.55	Remote Similarity	NPC469759
0.55	Remote Similarity	NPC160261
0.55	Remote Similarity	NPC221022
0.5238	Remote Similarity	NPC177022

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC63172 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8003
0.1-0.2	1055
0.2-0.3	81
0.3-0.4	8
0.4-0.5	0
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	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD2272	Phase 4
1.0	High Similarity	NPD5383	Phase 4

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