NPASS Compound

Natural Product: NPC17388

Natural Product ID	NPC17388
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	N-(3-Methoxybenzyl)Palmitamide
IUPAC Name	N-[(3-methoxyphenyl)methyl]hexadecanamide
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2415103
PubChem CID	71765531
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002341] Phenol ethers [CHEMONTID:0000138] Anisoles

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 68 68 0 0 0 0 0 0 0 0999 V2000 -4.6678 2.1624 -1.3381 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0130 1.5932 -1.6687 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9597 0.2894 -2.4103 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2676 -0.8165 -1.6947 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8419 -1.2066 -0.3881 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0762 -2.3378 0.2439 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6446 -1.9233 0.4592 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5015 -0.7089 1.3586 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9979 -0.4343 1.4729 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7265 0.7428 2.3405 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2917 1.0651 2.5188 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5438 1.4880 1.3969 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7570 0.6328 0.2178 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3332 -0.7335 0.4893 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6907 -0.6489 1.1533 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1845 -2.0408 1.3792 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1670 -2.6088 0.9492 N 0 0 0 0 0 0 0 0 0 0 0 0 5.2606 -2.4553 0.1569 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4331 -1.1146 -0.4470 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8828 -0.7894 -1.6856 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0537 0.4437 -2.2782 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8002 1.4053 -1.6255 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3584 1.1167 -0.3991 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1764 -0.1278 0.1815 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1039 2.0687 0.2590 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2997 3.3396 -0.3162 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3521 -2.8525 2.2602 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6571 2.3283 -0.2201 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5205 3.1364 -1.8012 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8254 1.4713 -1.5302 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5138 2.3181 -2.3490 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6877 1.5440 -0.7763 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4228 0.4762 -3.3641 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9989 0.0229 -2.6928 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2448 -1.6942 -2.3732 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1985 -0.5295 -1.5393 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8956 -1.5639 -0.4460 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8097 -0.3569 0.3445 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0647 -3.2024 -0.4578 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5100 -2.6108 1.2279 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1157 -2.8044 0.9553 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0775 -1.7928 -0.4846 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9397 0.1691 0.8419 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9834 -0.8762 2.3192 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6147 -0.3509 0.4751 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5887 -1.3624 1.9705 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1587 0.5861 3.3842 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2840 1.6424 1.9538 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1455 0.1888 3.0917 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1961 1.8950 3.3134 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1061 2.4664 0.9857 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5549 1.8585 1.7662 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0013 0.6718 -0.5743 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6539 1.1549 -0.3360 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4782 -1.2318 -0.4917 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7120 -1.3860 1.0980 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5159 -0.2232 2.1785 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4084 -0.0622 0.5974 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2531 -2.6516 0.7131 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2448 -3.1971 -0.7109 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3073 -1.5749 -2.1566 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6054 0.6683 -3.2588 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9114 2.3650 -2.1258 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6149 -0.3593 1.1469 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6294 4.0464 0.4857 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0967 3.3461 -1.0883 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3420 3.7697 -0.7137 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3184 -3.8442 2.0629 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 2 3 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 16 27 1 0 24 19 1 0 1 28 1 0 1 29 1 0 1 30 1 0 2 31 1 0 2 32 1 0 3 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 6 40 1 0 7 41 1 0 7 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 10 47 1 0 10 48 1 0 11 49 1 0 11 50 1 0 12 51 1 0 12 52 1 0 13 53 1 0 13 54 1 0 14 55 1 0 14 56 1 0 15 57 1 0 15 58 1 0 18 59 1 0 18 60 1 0 20 61 1 0 21 62 1 0 22 63 1 0 24 64 1 0 26 65 1 0 26 66 1 0 26 67 1 0 27 68 1 0 M END

Standard InCHIKey	FIQGQTITXPTKIY-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C24H41NO2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-19-24(26)25-21-22-17-16-18-23(20-22)27-2/h16-18,20H,3-15,19,21H2,1-2H3,(H,25,26)
SMILES	CCCCCCCCCCCCCCCC(=NCc1cccc(c1)OC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	375.31	Volume:	433.135 ? Van der Waals volume.
Dense:	0.866	LogP:	7.19 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.316 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.626 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	17.0	Rigid Bonds:	7.0
TPSA:	41.82 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	1.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.173	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.272	Fsp³:	0.708
MCE-18:	6.0 ? 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:	0.674	Fluc inhibitor:	0.155 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.462 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.022	Promiscuous compounds:	0.079

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.037	MDCK Permeability:	-4.798
Pgp-inhibitor:	0.028	Pgp-substrate:	0.002
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):	0.805
20% Bioavailability (F20%):	0.858	30% Bioavailability (F30%):	0.95
50% Bioavailability (F50%):	0.435

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012	MRP1:	0.842
Plasma Protein Binding (PPB):	99.312%	Volume Distribution (VD):	1.215
Fu:	0.958% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.867
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.049
BSEP inhibitor:	0.959

ADMET: Metabolism

CYP1A2-inhibitor:	0.059	CYP1A2-substrate:	0.902
CYP2C19-inhibitor:	0.939	CYP2C19-substrate:	0.413
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.866
CYP2D6-inhibitor:	0.999	CYP2D6-substrate:	0.133
CYP3A4-inhibitor:	0.112	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.99	CYP2C8-inhibitor:	0.963
HLM stability:	0.101 ? 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):

5.268

Half-life (T1/2):

0.579

ADMET: Toxicity

hERG Blockers:	0.403	hERG Blockers (10um):	0.758
Human Hepatotoxicity (H-HT):	0.911	Drug-induced Liver Injury (DILI):	0.825
AMES Toxicity:	0.435	Rat Oral Acute Toxicity:	0.134
Maximum Recommended Daily Dose:	0.571	Skin Sensitization:	0.999
Carcinogencity:	0.855	Eye Corrosion:	0.01
Eye Irritation:	0.944	Respiratory Toxicity:	0.966
Drug-induced Neurotoxicity:	0.228	Ototoxicity:	0.292
Hematotoxicity:	0.368	Drug-induced Nephrotoxicity:	0.733
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.011
A549 Cytotoxicity:	0.082	Hek293 Cytotoxicity:	0.114
BCF:	1.331 ? 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:	5.248 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.485 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.298 ? 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
NPO18988	Lepidium meyenii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932133]
NPO18988	Lepidium meyenii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23891163]
NPO18988	Lepidium meyenii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24972328]
NPO18988	Lepidium meyenii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33320645]
NPO18988	Lepidium meyenii	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18988	Lepidium meyenii	Species	Brassicaceae	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
Inhibition	2
IC50	3

Activity Type	# Activity
Individual protein	4
Single protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1418	Individual protein	Anandamide amidohydrolase	Homo sapiens	Inhibition	=	40.0	%	PMID[16933872]
NPT1418	Individual protein	Anandamide amidohydrolase	Homo sapiens	Inhibition	=	70.1	%	PMID[9090869]
NPT862	Individual protein	Epoxide hydratase	Homo sapiens	IC50	=	235.0	nM	PMID[33320645]
NPT21303	Single protein	Epoxide hydratase	Mus musculus	IC50	=	159.0	nM	PMID[33320645]
NPT5882	Individual protein	Epoxide hydrolase 2	Rattus norvegicus	IC50	=	113.0	nM	PMID[33320645]

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 NPC17388 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	21762
0.1-0.2	26541
0.2-0.3	1483
0.3-0.4	39
0.4-0.5	7
0.5-0.6	7
0.6-0.7	8
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471308
1.0	High Similarity	NPC483618
0.8723	High Similarity	NPC53596
0.82	Intermediate Similarity	NPC289330
0.7647	Intermediate Similarity	NPC483619
0.75	Intermediate Similarity	NPC160120
0.7308	Intermediate Similarity	NPC471314
0.7234	Intermediate Similarity	NPC74427
0.7115	Intermediate Similarity	NPC471315
0.7115	Intermediate Similarity	NPC483620
0.6591	Remote Similarity	NPC471307
0.6591	Remote Similarity	NPC78041
0.6591	Remote Similarity	NPC141139
0.6346	Remote Similarity	NPC285078
0.6346	Remote Similarity	NPC130595
0.6346	Remote Similarity	NPC93882
0.6346	Remote Similarity	NPC255540
0.6071	Remote Similarity	NPC483621
0.58	Remote Similarity	NPC74936
0.58	Remote Similarity	NPC159178
0.569	Remote Similarity	NPC6854
0.5517	Remote Similarity	NPC483622
0.5472	Remote Similarity	NPC209764
0.5439	Remote Similarity	NPC218530
0.5254	Remote Similarity	NPC202613

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC17388 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2308
0.1-0.2	6247
0.2-0.3	578
0.3-0.4	13
0.4-0.5	2
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
0.6346	Remote Similarity	NPD2674	Phase 3
0.5484	Remote Similarity	NPD7153	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