NPASS Compound

Natural Product: NPC554292

Natural Product ID	NPC554292
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	7-oxooctadec-11-enoic acid
IUPAC Name	7-oxooctadec-11-enoic acid
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 53 52 0 0 0 0 0 0 0 0999 V2000 -5.9273 0.4921 3.2738 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6179 1.0224 1.9038 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4515 -0.0315 0.8650 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3453 -1.0038 1.1411 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9948 -0.3699 1.2482 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6053 0.3623 -0.0529 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5812 -0.6027 -1.1554 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5567 -0.9056 -1.8974 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2114 -0.3065 -1.7415 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1368 0.3905 -3.0397 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4707 1.0538 -3.0493 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6214 0.1476 -2.8377 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4975 -1.0656 -2.6898 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9675 0.7917 -2.8122 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2849 1.1485 -1.3831 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2916 -0.0933 -0.5578 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6198 0.2085 0.9103 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5927 -1.1262 1.6244 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8878 -1.0199 3.0486 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9016 -2.0452 3.7643 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1529 0.2090 3.6147 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4269 -0.4394 3.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0341 0.2995 3.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6260 1.2766 4.0261 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7608 1.7476 1.9171 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5006 1.6451 1.5985 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3979 -0.6159 0.8216 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3465 0.4580 -0.1191 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3489 -1.7725 0.3428 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5301 -1.5549 2.0832 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2372 -1.1758 1.3500 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8881 0.2837 2.1211 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4205 1.1386 -0.1998 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6970 0.9478 0.1080 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5265 -1.1458 -1.4056 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6636 -1.6700 -2.7220 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2183 0.3961 -0.9043 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5501 -1.0797 -1.4707 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6249 1.1955 -3.1762 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0845 -0.3088 -3.8908 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6075 1.5062 -4.0599 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4629 1.8516 -2.2710 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7241 0.0409 -3.1242 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9630 1.6786 -3.4759 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3182 1.5919 -1.3049 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6104 1.9387 -0.9857 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3236 -0.6499 -0.5773 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1065 -0.7527 -0.9193 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6634 0.6318 0.8879 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9305 0.9466 1.3345 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5990 -1.5798 1.4067 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3690 -1.7610 1.1044 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8013 0.3007 4.4037 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 10 11 1 0 11 12 1 0 12 13 2 0 12 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 2 0 19 21 1 0 1 22 1 0 1 23 1 0 1 24 1 0 2 25 1 0 2 26 1 0 3 27 1 0 3 28 1 0 4 29 1 0 4 30 1 0 5 31 1 0 5 32 1 0 6 33 1 0 6 34 1 0 7 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 14 43 1 0 14 44 1 0 15 45 1 0 15 46 1 0 16 47 1 0 16 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	VWEWTQPRFPEQEU-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C18H32O3/c1-2-3-4-5-6-7-8-9-11-14-17(19)15-12-10-13-16-18(20)21/h7-8H,2-6,9-16H2,1H3,(H,20,21)
SMILES	CCCCCCC=CCCCC(=O)CCCCCC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	296.24	Volume:	338.345 ? Van der Waals volume.
Dense:	0.876	LogP:	5.376 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.407 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.361 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	3.0
TPSA:	54.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	0.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.33	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.22	Fsp³:	0.778
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:	0.007	Fluc inhibitor:	0.241 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.011 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.993	Promiscuous compounds:	0.915

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.183	MDCK Permeability:	-4.811
Pgp-inhibitor:	0.0	Pgp-substrate:	0.013
PAMPA:	0.473 ? 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):	0.308
20% Bioavailability (F20%):	0.068	30% Bioavailability (F30%):	0.182
50% Bioavailability (F50%):	0.093

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019	MRP1:	0.965
Plasma Protein Binding (PPB):	97.371%	Volume Distribution (VD):	-0.571
Fu:	1.932% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.023
OATP1B3 inhibitor:	0.985	BCRP inhibitor:	0.009
BSEP inhibitor:	0.683

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.635
CYP2C19-inhibitor:	0.849	CYP2C19-substrate:	0.899
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.049	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.881
CYP2B6-substrate:	1.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.074 ? 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):

3.967

Half-life (T1/2):

0.482

ADMET: Toxicity

hERG Blockers:	0.148	hERG Blockers (10um):	0.356
Human Hepatotoxicity (H-HT):	0.234	Drug-induced Liver Injury (DILI):	0.008
AMES Toxicity:	0.07	Rat Oral Acute Toxicity:	0.045
Maximum Recommended Daily Dose:	0.163	Skin Sensitization:	0.992
Carcinogencity:	0.081	Eye Corrosion:	0.995
Eye Irritation:	0.996	Respiratory Toxicity:	0.773
Drug-induced Neurotoxicity:	0.013	Ototoxicity:	0.34
Hematotoxicity:	0.103	Drug-induced Nephrotoxicity:	0.496
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.044
A549 Cytotoxicity:	0.046	Hek293 Cytotoxicity:	0.064
BCF:	1.175 ? 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:	3.922 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.214 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.223 ? 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
NPO24316	Salvia mirzayanii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20857430]
NPO23251	Polygala glomerata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13643	Rhamnus japonica	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24316	Salvia mirzayanii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23422	Tephrosia procumbens	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23251	Polygala glomerata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24316	Salvia mirzayanii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13643	Rhamnus japonica	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23422	Tephrosia procumbens	Species	Geometridae	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 NPC554292 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	33189
0.1-0.2	14915
0.2-0.3	1380
0.3-0.4	213
0.4-0.5	79
0.5-0.6	41
0.6-0.7	12
0.7-0.8	3
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
0.9167	High Similarity	NPC477201
0.7941	Intermediate Similarity	NPC18712
0.7941	Intermediate Similarity	NPC74845
0.7692	Intermediate Similarity	NPC106851
0.7692	Intermediate Similarity	NPC282788
0.7692	Intermediate Similarity	NPC274927
0.7647	Intermediate Similarity	NPC424
0.7647	Intermediate Similarity	NPC36061
0.7647	Intermediate Similarity	NPC69510
0.7647	Intermediate Similarity	NPC77272
0.7647	Intermediate Similarity	NPC290563
0.7647	Intermediate Similarity	NPC139029
0.7647	Intermediate Similarity	NPC281972
0.7647	Intermediate Similarity	NPC261831
0.7647	Intermediate Similarity	NPC87564
0.7353	Intermediate Similarity	NPC281245
0.7317	Intermediate Similarity	NPC251042
0.7317	Intermediate Similarity	NPC174447
0.7317	Intermediate Similarity	NPC122521
0.7143	Intermediate Similarity	NPC92114
0.7027	Intermediate Similarity	NPC154245
0.7027	Intermediate Similarity	NPC85813
0.7027	Intermediate Similarity	NPC223697
0.7027	Intermediate Similarity	NPC6095
0.6944	Remote Similarity	NPC95145
0.6944	Remote Similarity	NPC325642
0.6944	Remote Similarity	NPC65174
0.6757	Remote Similarity	NPC321062
0.6667	Remote Similarity	NPC40082
0.6316	Remote Similarity	NPC5413
0.6222	Remote Similarity	NPC329550
0.6154	Remote Similarity	NPC52955
0.6154	Remote Similarity	NPC88966
0.6154	Remote Similarity	NPC25417
0.6154	Remote Similarity	NPC1813
0.6154	Remote Similarity	NPC59051
0.5897	Remote Similarity	NPC91495
0.5897	Remote Similarity	NPC70387
0.5882	Remote Similarity	NPC171736
0.5882	Remote Similarity	NPC301585
0.5882	Remote Similarity	NPC261080
0.5882	Remote Similarity	NPC132565
0.5882	Remote Similarity	NPC209970
0.5882	Remote Similarity	NPC216630
0.5882	Remote Similarity	NPC201844
0.5882	Remote Similarity	NPC301696
0.5882	Remote Similarity	NPC196924
0.5882	Remote Similarity	NPC307783
0.5882	Remote Similarity	NPC154186
0.5882	Remote Similarity	NPC149184
0.5882	Remote Similarity	NPC279026
0.5882	Remote Similarity	NPC113928
0.5882	Remote Similarity	NPC14227
0.587	Remote Similarity	NPC325977
0.587	Remote Similarity	NPC235242
0.5778	Remote Similarity	NPC243532
0.5652	Remote Similarity	NPC68343
0.5652	Remote Similarity	NPC328089
0.5588	Remote Similarity	NPC155263
0.5581	Remote Similarity	NPC606120
0.5556	Remote Similarity	NPC179764
0.5435	Remote Similarity	NPC255863
0.5435	Remote Similarity	NPC473863
0.5435	Remote Similarity	NPC136164
0.5435	Remote Similarity	NPC245947
0.5405	Remote Similarity	NPC180534
0.5405	Remote Similarity	NPC611531
0.5319	Remote Similarity	NPC318420
0.5319	Remote Similarity	NPC326268
0.5306	Remote Similarity	NPC322461
0.525	Remote Similarity	NPC149821
0.5227	Remote Similarity	NPC487561
0.5227	Remote Similarity	NPC225929
0.5128	Remote Similarity	NPC34416
0.5111	Remote Similarity	NPC482480
0.5111	Remote Similarity	NPC482481
0.5098	Remote Similarity	NPC258824

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC554292 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6202
0.1-0.2	2700
0.2-0.3	198
0.3-0.4	26
0.4-0.5	11
0.5-0.6	6
0.6-0.7	3
0.7-0.8	3
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
0.7647	Intermediate Similarity	NPD3195	Phase 2
0.7647	Intermediate Similarity	NPD3196	Approved
0.7027	Intermediate Similarity	NPD4266	Phase 2
0.6341	Remote Similarity	NPD3194	Phase 4
0.6316	Remote Similarity	NPD3173	Phase 4
0.6154	Remote Similarity	NPD3172	Approved
0.5882	Remote Similarity	NPD2270	Pre-clinical
0.5882	Remote Similarity	NPD633	Phase 3
0.5882	Remote Similarity	NPD9448	Phase 2
0.5686	Remote Similarity	NPD5368	Phase 2
0.5652	Remote Similarity	NPD39	Phase 4
0.5405	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