NPASS Compound

Natural Product: NPC54000

Natural Product ID	NPC54000
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HRALRUDVSKRSQK-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44203446
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002949] Long-chain fatty acids

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 53 52 0 0 0 0 0 0 0 0999 V2000 7.7755 -0.3492 -2.1007 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8330 0.0238 -1.2777 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1785 -0.5139 0.2301 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2211 -1.5483 0.6370 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7238 -1.2305 0.7954 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1990 -0.6436 -0.4245 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6671 -0.5193 -0.4243 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2460 0.2694 0.7528 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7508 0.5060 0.8421 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1957 1.0783 -0.4028 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1336 1.6908 -0.1886 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2193 0.8777 0.4186 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4884 -0.3559 -0.3176 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7212 -0.9908 0.4453 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8479 -0.3569 -0.0369 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1198 0.3500 -0.5903 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0971 0.9149 -1.0296 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0917 1.3894 0.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7541 0.1230 0.4779 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6669 -0.9282 0.0111 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.6202 0.3635 1.6366 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5498 -0.6721 -2.6952 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7631 -0.5918 -1.1198 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0508 0.5742 -1.4783 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1948 -0.6011 0.3154 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9597 0.5545 0.6988 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4506 -2.5124 0.2623 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5095 -1.5956 1.8822 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2567 -2.2757 0.9084 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5590 -0.6870 1.7231 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5346 0.4510 -0.3755 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4808 -1.0651 -1.3721 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5004 0.2241 -1.3386 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1282 -1.4034 -0.5784 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4361 -0.4271 1.6582 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8470 1.1693 0.9275 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2420 -0.5274 0.9246 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5383 1.0072 1.7473 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8344 1.7395 -0.9809 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0048 0.1053 -1.0721 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9990 2.6460 0.4025 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4768 2.0989 -1.1955 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8916 0.5611 1.4772 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0637 1.5089 0.6195 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6536 -1.0037 -0.5039 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9007 -0.1510 -1.3504 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8031 -2.0985 0.5453 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5897 -0.5028 1.5354 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7966 0.3190 -1.7488 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8975 1.9123 -1.6033 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7779 2.2192 -0.2649 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4506 1.8237 0.8934 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.5608 -0.0324 1.6098 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 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 3 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 3 25 1 0 3 26 1 0 4 27 1 0 4 28 1 0 5 29 1 0 5 30 1 0 6 31 1 0 6 32 1 0 7 33 1 0 7 34 1 0 8 35 1 0 8 36 1 0 9 37 1 0 9 38 1 0 10 39 1 0 10 40 1 0 11 41 1 0 11 42 1 0 12 43 1 0 12 44 1 0 13 45 1 0 13 46 1 0 14 47 1 0 14 48 1 0 17 49 1 0 17 50 1 0 18 51 1 0 18 52 1 0 21 53 1 0 M END

Standard InCHIKey	HRALRUDVSKRSQK-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C19H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19(20)21/h2H,1,3-14,17-18H2,(H,20,21)
SMILES	C=CCCCCCCCCCCCCC#CCCC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	292.24	Volume:	344.215 ? Van der Waals volume.
Dense:	0.849	LogP:	6.016 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.455 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.327 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	3.0
TPSA:	37.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	1.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.252	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.463	Fsp³:	0.737
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:	0.084	Fluc inhibitor:	0.02 ? 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:	0.008 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.986	Promiscuous compounds:	0.444

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.079	MDCK Permeability:	-4.725
Pgp-inhibitor:	0.001	Pgp-substrate:	0.0
PAMPA:	0.336 ? 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):	0.288
20% Bioavailability (F20%):	0.139	30% Bioavailability (F30%):	0.456
50% Bioavailability (F50%):	0.233

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.023	MRP1:	0.84
Plasma Protein Binding (PPB):	99.29%	Volume Distribution (VD):	0.467
Fu:	0.34% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.821
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.439
BSEP inhibitor:	0.774

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.558	CYP2C19-substrate:	0.995
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.046	CYP2D6-substrate:	0.295
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.006
CYP2B6-substrate:	0.146	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? 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):

3.594

Half-life (T1/2):

0.997

ADMET: Toxicity

hERG Blockers:	0.033	hERG Blockers (10um):	0.206
Human Hepatotoxicity (H-HT):	0.274	Drug-induced Liver Injury (DILI):	0.06
AMES Toxicity:	0.185	Rat Oral Acute Toxicity:	0.282
Maximum Recommended Daily Dose:	0.574	Skin Sensitization:	0.999
Carcinogencity:	0.288	Eye Corrosion:	0.998
Eye Irritation:	0.998	Respiratory Toxicity:	0.977
Drug-induced Neurotoxicity:	0.042	Ototoxicity:	0.252
Hematotoxicity:	0.098	Drug-induced Nephrotoxicity:	0.177
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.026
A549 Cytotoxicity:	0.006	Hek293 Cytotoxicity:	0.076
BCF:	1.042 ? 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:	3.958 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.61 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.257 ? 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
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520235]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1254564]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18855442]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20192236]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26195800]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8626242]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10807	Melanothamnus somalensis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3376	Eriostemon brucei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7106	Talaromyces helicus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3376	Eriostemon brucei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18675	Pteris aquilina	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11305	Garcinia cantleyana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10967	Parmelia gigas	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6430	Cercosporina kikuchii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10807	Melanothamnus somalensis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11827	Zerynthia polyxena	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	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 NPC54000 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	42196
0.1-0.2	6814
0.2-0.3	660
0.3-0.4	146
0.4-0.5	33
0.5-0.6	9
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	Natural Product ID
0.625	Remote Similarity	NPC485704
0.5758	Remote Similarity	NPC180534
0.5758	Remote Similarity	NPC611531
0.5641	Remote Similarity	NPC18357
0.5278	Remote Similarity	NPC129972
0.5278	Remote Similarity	NPC8219
0.5278	Remote Similarity	NPC301528
0.5278	Remote Similarity	NPC71317
0.5278	Remote Similarity	NPC163746
0.5278	Remote Similarity	NPC103286

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC54000 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7236
0.1-0.2	1760
0.2-0.3	134
0.3-0.4	17
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
0.5758	Remote Similarity	NPD622	Pre-clinical

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