NPASS Compound

Natural Product: NPC114067

Natural Product ID	NPC114067
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JELGPLUONQGOHF-KTKRTIGZSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6436624
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000324] Fatty acid esters

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 54 53 0 0 0 0 0 0 0 0999 V2000 6.5908 -1.6181 1.5490 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8229 -1.9333 0.2834 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7543 -0.8606 0.0307 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4224 0.4615 -0.1125 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4825 1.6070 -0.3470 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7153 1.3673 -1.6367 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7853 2.4708 -1.9196 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4942 2.3609 -2.0251 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8037 1.0648 -1.8635 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1722 1.2128 -0.7038 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9363 -0.0906 -0.4583 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8635 0.1874 0.7057 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6973 -1.0130 1.0834 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5712 -0.6063 2.2440 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4951 0.5262 1.9557 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4605 0.2773 0.8707 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2611 1.2066 0.5265 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5762 -0.9013 0.1794 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5124 -1.0931 -0.8477 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8990 -0.8940 -0.2839 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9270 -2.5601 2.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9397 -1.0960 2.2765 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4496 -0.9497 1.3501 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2679 -2.8829 0.4360 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4927 -2.0364 -0.5719 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0241 -0.9099 0.8537 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2718 -1.1628 -0.9169 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0570 0.4011 -1.0487 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1584 0.6719 0.6946 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6970 1.6063 0.4604 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9648 2.5835 -0.3278 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3127 0.3623 -1.7077 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4762 1.4143 -2.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2250 3.4805 -2.0542 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8623 3.2708 -2.2464 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4412 0.2123 -1.6280 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2560 0.7815 -2.7989 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9282 1.9923 -0.9211 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3698 1.5269 0.2074 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2523 -0.9249 -0.2112 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5708 -0.3411 -1.3324 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2474 0.4478 1.5896 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5449 0.9875 0.3821 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3181 -1.4090 0.2810 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0568 -1.8475 1.4662 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1898 -1.4860 2.5430 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9293 -0.2902 3.1039 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9654 1.4810 1.7576 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0865 0.7123 2.8898 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3949 -0.3271 -1.6691 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4182 -2.1126 -1.2781 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8252 -0.9576 0.8196 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5533 -1.7489 -0.5810 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3390 0.0792 -0.6060 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 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 0 16 18 1 0 18 19 1 0 19 20 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 5 31 1 0 6 32 1 0 6 33 1 0 7 34 1 0 8 35 1 0 9 36 1 0 9 37 1 0 10 38 1 0 10 39 1 0 11 40 1 0 11 41 1 0 12 42 1 0 12 43 1 0 13 44 1 0 13 45 1 0 14 46 1 0 14 47 1 0 15 48 1 0 15 49 1 0 19 50 1 0 19 51 1 0 20 52 1 0 20 53 1 0 20 54 1 0 M END

Standard InCHIKey	JELGPLUONQGOHF-KTKRTIGZSA-N
Standard InCHI	InChI=1S/C18H34O2/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20-4-2/h9-10H,3-8,11-17H2,1-2H3/b10-9-
SMILES	CCCCCC/C=CCCCCCCCC(=O)OCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	282.26	Volume:	332.192 ? Van der Waals volume.
Dense:	0.85	LogP:	6.835 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.145 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.574 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	2.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.228	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.042	Fsp³:	0.833
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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.062	Fluc inhibitor:	0.029 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.009 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.997	Promiscuous compounds:	0.333

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.014	MDCK Permeability:	-4.66
Pgp-inhibitor:	0.853	Pgp-substrate:	0.001
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):	0.015
20% Bioavailability (F20%):	0.554	30% Bioavailability (F30%):	0.757
50% Bioavailability (F50%):	0.905

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013	MRP1:	0.996
Plasma Protein Binding (PPB):	98.404%	Volume Distribution (VD):	-0.564
Fu:	0.935% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.011
OATP1B3 inhibitor:	0.99	BCRP inhibitor:	0.424
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.982
CYP2C9-inhibitor:	0.446	CYP2C9-substrate:	0.294
CYP2D6-inhibitor:	0.066	CYP2D6-substrate:	0.999
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.049	CYP2C8-inhibitor:	1.0
HLM stability:	0.784 ? 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):

5.575

Half-life (T1/2):

0.293

ADMET: Toxicity

hERG Blockers:	0.298	hERG Blockers (10um):	0.738
Human Hepatotoxicity (H-HT):	0.141	Drug-induced Liver Injury (DILI):	0.006
AMES Toxicity:	0.101	Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.121	Skin Sensitization:	0.999
Carcinogencity:	0.184	Eye Corrosion:	0.997
Eye Irritation:	0.997	Respiratory Toxicity:	0.492
Drug-induced Neurotoxicity:	0.008	Ototoxicity:	0.111
Hematotoxicity:	0.023	Drug-induced Nephrotoxicity:	0.279
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.043
A549 Cytotoxicity:	0.212	Hek293 Cytotoxicity:	0.133
BCF:	1.427 ? 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:	4.701 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.893 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.031 ? 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
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21620	Thlaspi arvense	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

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 NPC114067 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	24294
0.1-0.2	22869
0.2-0.3	2140
0.3-0.4	409
0.4-0.5	81
0.5-0.6	34
0.6-0.7	14
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC128061
0.8966	High Similarity	NPC28779
0.7742	Intermediate Similarity	NPC10316
0.7742	Intermediate Similarity	NPC200845
0.7742	Intermediate Similarity	NPC223677
0.7692	Intermediate Similarity	NPC250028
0.7692	Intermediate Similarity	NPC236579
0.7692	Intermediate Similarity	NPC80234
0.7692	Intermediate Similarity	NPC203531
0.7692	Intermediate Similarity	NPC256163
0.7692	Intermediate Similarity	NPC40597
0.7273	Intermediate Similarity	NPC277597
0.7241	Intermediate Similarity	NPC309606
0.7143	Intermediate Similarity	NPC143857
0.7143	Intermediate Similarity	NPC229252
0.7059	Intermediate Similarity	NPC104537
0.6923	Remote Similarity	NPC53541
0.6667	Remote Similarity	NPC475443
0.6667	Remote Similarity	NPC473829
0.6562	Remote Similarity	NPC71761
0.6562	Remote Similarity	NPC39633
0.6486	Remote Similarity	NPC330426
0.6486	Remote Similarity	NPC127091
0.6486	Remote Similarity	NPC22101
0.6316	Remote Similarity	NPC54925
0.625	Remote Similarity	NPC228473
0.6154	Remote Similarity	NPC48218
0.6154	Remote Similarity	NPC141481
0.6154	Remote Similarity	NPC464342
0.6129	Remote Similarity	NPC310746
0.5833	Remote Similarity	NPC148192
0.5806	Remote Similarity	NPC600941
0.5806	Remote Similarity	NPC603612
0.5789	Remote Similarity	NPC321919
0.5789	Remote Similarity	NPC476654
0.5789	Remote Similarity	NPC476655
0.5789	Remote Similarity	NPC476656
0.5714	Remote Similarity	NPC473559
0.5714	Remote Similarity	NPC324981
0.5641	Remote Similarity	NPC271921
0.5625	Remote Similarity	NPC149299
0.5588	Remote Similarity	NPC163345
0.5588	Remote Similarity	NPC139545
0.5556	Remote Similarity	NPC143211
0.5455	Remote Similarity	NPC26253
0.5312	Remote Similarity	NPC80396
0.5312	Remote Similarity	NPC154642
0.5294	Remote Similarity	NPC488257
0.5294	Remote Similarity	NPC469937
0.5294	Remote Similarity	NPC94699
0.5294	Remote Similarity	NPC320588
0.5294	Remote Similarity	NPC53463
0.525	Remote Similarity	NPC209327
0.5238	Remote Similarity	NPC473772
0.5172	Remote Similarity	NPC201622
0.5172	Remote Similarity	NPC305660
0.5172	Remote Similarity	NPC12156
0.5172	Remote Similarity	NPC161097
0.5172	Remote Similarity	NPC28598
0.5172	Remote Similarity	NPC22903
0.5172	Remote Similarity	NPC54980
0.5143	Remote Similarity	NPC55678
0.5128	Remote Similarity	NPC476660
0.5122	Remote Similarity	NPC273508

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC114067 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6808
0.1-0.2	2156
0.2-0.3	144
0.3-0.4	34
0.4-0.5	4
0.5-0.6	2
0.6-0.7	2
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
0.6562	Remote Similarity	NPD5343	Phase 4
0.6176	Remote Similarity	NPD6096	Phase 4
0.5455	Remote Similarity	NPD6097	Approved
0.5143	Remote Similarity	NPD6125	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