NPASS Compound

Natural Product: NPC328960

Natural Product ID	NPC328960
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GGJRAQULURVTAJ-KYNNUBNZSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5317746
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids and derivatives

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 61 60 0 0 0 0 0 0 0 0999 V2000 -5.8070 -3.1762 -0.5375 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7103 -1.6611 -0.6905 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0300 -1.0534 -0.5709 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3979 -0.1782 0.3225 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4780 0.3265 1.3718 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3696 1.7860 1.1810 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 2.3921 0.9237 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8999 1.8056 0.7706 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4184 2.1369 -0.5913 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3383 2.8242 -0.8284 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4133 3.3891 0.1680 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0140 2.7806 -0.0587 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1789 1.2886 0.1161 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1176 0.5450 -0.0792 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1729 0.9700 0.8926 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4701 0.2520 0.7223 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0838 0.4521 -0.6407 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3715 -0.2768 -0.7645 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3742 0.2353 -0.2256 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4673 -1.4622 -1.4392 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6628 -2.1605 -1.5613 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1710 -2.5780 -0.2084 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4745 -3.3457 -0.3549 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4095 -2.4837 -0.9357 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1848 -3.3959 0.3714 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7961 -3.6216 -0.6083 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4377 -3.5352 -1.3743 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2971 -3.4158 0.4213 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3647 -1.4818 -1.7466 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9455 -1.2738 -0.0389 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7735 -1.3922 -1.3336 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4373 0.2024 0.2983 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4986 -0.1355 1.3944 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0021 0.1597 2.3759 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3260 2.3438 1.2734 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2887 3.5089 0.7989 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8920 0.6914 0.8480 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2296 2.1415 1.5779 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0584 1.7487 -1.4118 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1187 2.9845 -1.9183 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3403 4.5014 0.0982 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7012 3.1565 1.1897 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6553 3.1974 0.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3347 3.0688 -1.0539 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8733 0.9374 -0.6779 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5388 1.1105 1.1285 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4817 0.7464 -1.1085 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8957 -0.5322 0.0965 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7685 0.8447 1.9171 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3675 2.0775 0.7937 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2912 -0.8239 0.9121 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1997 0.5835 1.4800 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2530 1.4949 -0.8971 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3666 0.0376 -1.3950 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4656 -3.0444 -2.2097 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4359 -1.5779 -2.1168 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3606 -1.7074 0.4206 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3128 -4.1904 -1.0284 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8887 -3.6315 0.6328 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7449 -1.7969 -0.3213 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4366 -2.7894 0.6349 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 3 4 5 1 0 5 6 1 0 6 7 2 3 7 8 1 0 8 9 1 0 9 10 2 3 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 2 0 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 22 25 1 0 1 26 1 0 1 27 1 0 1 28 1 0 2 29 1 0 2 30 1 0 3 31 1 0 4 32 1 0 5 33 1 0 5 34 1 0 6 35 1 0 7 36 1 0 8 37 1 0 8 38 1 0 9 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 15 49 1 0 15 50 1 0 16 51 1 0 16 52 1 0 17 53 1 0 17 54 1 0 21 55 1 0 21 56 1 0 22 57 1 0 23 58 1 0 23 59 1 0 24 60 1 0 25 61 1 0 M END

Standard InCHIKey	GGJRAQULURVTAJ-KYNNUBNZSA-N
Standard InCHI	InChI=1S/C21H36O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h3-4,6-7,9-10,20,22-23H,2,5,8,11-19H2,1H3/b4-3+,7-6+,10-9-
SMILES	CCC=CCC=CCC=CCCCCCCCC(=O)OCC(CO)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	352.26	Volume:	396.387 ? Van der Waals volume.
Dense:	0.889	LogP:	4.489 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.375 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.76 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	17.0	Rigid Bonds:	4.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	0.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.244	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.211	Fsp³:	0.667
MCE-18:	2.0 ? 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:	0.076	Fluc inhibitor:	0.004 ? 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:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.813	Promiscuous compounds:	0.03

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.08	MDCK Permeability:	-4.854
Pgp-inhibitor:	0.001	Pgp-substrate:	0.049
PAMPA:	0.183 ? 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):	0.093
20% Bioavailability (F20%):	0.631	30% Bioavailability (F30%):	0.848
50% Bioavailability (F50%):	0.869

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.188	MRP1:	0.921
Plasma Protein Binding (PPB):	97.279%	Volume Distribution (VD):	-0.35
Fu:	3.248% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.03
OATP1B3 inhibitor:	0.667	BCRP inhibitor:	0.084
BSEP inhibitor:	0.835

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.425
CYP2C19-inhibitor:	0.004	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.999	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.558	CYP2C8-inhibitor:	1.0
HLM stability:	0.088 ? 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):

5.957

Half-life (T1/2):

0.385

ADMET: Toxicity

hERG Blockers:	0.083	hERG Blockers (10um):	0.329
Human Hepatotoxicity (H-HT):	0.063	Drug-induced Liver Injury (DILI):	0.001
AMES Toxicity:	0.79	Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.036	Skin Sensitization:	1.0
Carcinogencity:	0.341	Eye Corrosion:	0.294
Eye Irritation:	0.913	Respiratory Toxicity:	0.145
Drug-induced Neurotoxicity:	0.023	Ototoxicity:	0.674
Hematotoxicity:	0.009	Drug-induced Nephrotoxicity:	0.24
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.018
A549 Cytotoxicity:	0.033	Hek293 Cytotoxicity:	0.022
BCF:	1.664 ? 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:	4.724 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.112 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.026 ? 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
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	seeds	n.a.	n.a.	PMID[11858758]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19649	Akebia quinata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18781	Hyoscyamus niger	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19649	Akebia quinata	Species	Lardizabalaceae	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 NPC328960 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	15642
0.1-0.2	31024
0.2-0.3	2786
0.3-0.4	313
0.4-0.5	47
0.5-0.6	19
0.6-0.7	15
0.7-0.8	0
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC271921
0.8919	High Similarity	NPC330426
0.8919	High Similarity	NPC127091
0.8919	High Similarity	NPC22101
0.8158	Intermediate Similarity	NPC321919
0.8108	Intermediate Similarity	NPC104537
0.7381	Intermediate Similarity	NPC473772
0.7297	Intermediate Similarity	NPC10316
0.7297	Intermediate Similarity	NPC200845
0.725	Intermediate Similarity	NPC475443
0.725	Intermediate Similarity	NPC473829
0.7073	Intermediate Similarity	NPC209327
0.6905	Remote Similarity	NPC273508
0.6829	Remote Similarity	NPC476654
0.6829	Remote Similarity	NPC476655
0.6829	Remote Similarity	NPC476656
0.65	Remote Similarity	NPC277597
0.6486	Remote Similarity	NPC488257
0.6486	Remote Similarity	NPC469937
0.6486	Remote Similarity	NPC94699
0.6486	Remote Similarity	NPC320588
0.6486	Remote Similarity	NPC53463
0.641	Remote Similarity	NPC28779
0.6316	Remote Similarity	NPC139545
0.6304	Remote Similarity	NPC473559
0.6304	Remote Similarity	NPC324981
0.6	Remote Similarity	NPC609455
0.5918	Remote Similarity	NPC474321
0.5789	Remote Similarity	NPC236649
0.5778	Remote Similarity	NPC54925
0.5652	Remote Similarity	NPC48218
0.5652	Remote Similarity	NPC141481
0.5652	Remote Similarity	NPC464342
0.5641	Remote Similarity	NPC128061
0.5636	Remote Similarity	NPC489083
0.55	Remote Similarity	NPC39633
0.5333	Remote Similarity	NPC110813
0.5323	Remote Similarity	NPC38295
0.5254	Remote Similarity	NPC21693
0.5238	Remote Similarity	NPC223677
0.5156	Remote Similarity	NPC470313
0.5156	Remote Similarity	NPC473500
0.5156	Remote Similarity	NPC611497
0.5122	Remote Similarity	NPC71761
0.5111	Remote Similarity	NPC81896
0.5082	Remote Similarity	NPC133377

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC328960 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6079
0.1-0.2	2911
0.2-0.3	139
0.3-0.4	16
0.4-0.5	1
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
0.6316	Remote Similarity	NPD5343	Phase 4
0.6	Remote Similarity	NPD6096	Phase 4
0.5385	Remote Similarity	NPD6097	Approved
0.5106	Remote Similarity	NPD3728	Approved

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