NPASS Compound

Natural Product: NPC218324

Natural Product ID	NPC218324
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FERSMFQBWVBKQK-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	4479451
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002365] Cyanogenic glycosides

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 55 56 0 0 0 0 0 0 0 0999 V2000 -4.5806 2.7525 1.4379 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9340 2.4240 0.0774 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8101 2.8545 -1.0332 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6930 3.2488 0.0741 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6947 3.8878 0.0754 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.5588 1.0955 0.1226 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9489 0.7397 -1.0637 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4198 -0.4815 -1.7318 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9677 -1.7610 -1.1232 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5506 -1.6614 -0.7051 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1489 -0.3647 -0.1056 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3390 -0.2656 0.0301 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9572 -1.2875 0.7117 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -1.0296 0.7671 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1356 -2.1097 0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5750 -1.6322 0.1019 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9991 -1.2241 1.4904 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9946 -0.3980 2.2288 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2209 1.0911 1.9125 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5465 1.4616 2.1126 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6774 -0.7422 2.0636 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1786 -0.4767 1.3917 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6290 -0.5367 -0.7564 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6647 -2.6059 -1.0468 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5752 0.7432 -0.7852 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7452 -1.9834 -1.8185 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0630 -2.7311 -2.1595 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8381 -0.5052 -1.6794 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4151 3.8133 1.6415 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6341 2.4753 1.3395 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0399 2.1753 2.2401 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2559 3.4317 -1.8337 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5514 3.6316 -0.6435 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4535 2.1044 -1.5004 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0494 1.6004 -1.7623 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2020 -0.4453 -2.8305 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6583 -2.0352 -0.2955 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3427 -2.4822 0.0341 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5846 -0.3231 0.9158 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7952 -0.2886 -1.0049 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6071 0.7420 0.4290 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5012 -0.0816 0.1979 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1577 -2.9677 0.8736 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2023 -2.4285 -0.3197 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2639 -2.1569 2.0507 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2211 -0.5034 3.3060 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0401 1.2672 0.8185 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5936 1.7106 2.5738 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9958 1.8500 1.3488 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6860 -0.5710 2.2340 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0527 -0.6845 -1.5205 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4427 -1.8930 -1.6611 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9487 -2.9648 -1.9650 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9497 -2.3276 -3.0410 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1682 -1.1504 -2.3570 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 3 0 2 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 1 0 17 18 1 0 18 19 1 0 19 20 1 0 18 21 1 0 17 22 1 0 16 23 1 0 15 24 1 0 11 25 1 0 10 26 1 0 9 27 1 0 8 28 1 0 25 7 1 0 21 14 1 0 1 29 1 0 1 30 1 0 1 31 1 0 3 32 1 0 3 33 1 0 3 34 1 0 7 35 1 0 8 36 1 0 9 37 1 0 10 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 14 42 1 0 15 43 1 0 16 44 1 0 17 45 1 0 18 46 1 0 19 47 1 0 19 48 1 0 20 49 1 0 22 50 1 0 23 51 1 0 24 52 1 0 26 53 1 0 27 54 1 0 28 55 1 0 M END

Standard InCHIKey	FERSMFQBWVBKQK-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C16H27NO11/c1-16(2,5-17)28-15-13(24)11(22)9(20)7(27-15)4-25-14-12(23)10(21)8(19)6(3-18)26-14/h6-15,18-24H,3-4H2,1-2H3
SMILES	CC(C)(C#N)OC1C(C(C(C(COC2C(C(C(C(CO)O2)O)O)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	409.16	Volume:	370.596 ? Van der Waals volume.
Dense:	1.104	LogP:	-2.066 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.178 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.608 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	13.0
TPSA:	202.32 ? Topological Polar Surface Area.	H-Bond Acceptor:	12.0
H-Bond Donor:	7.0	Rings:	2.0
Heavy Atoms:	12.0

MedChem Properties

QED Drug-Likeness Score:	0.224	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.618	Fsp³:	0.938
MCE-18:	50.258 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.001	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.023 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.012 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.315	Promiscuous compounds:	0.005

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.155	MDCK Permeability:	-4.933
Pgp-inhibitor:	0.0	Pgp-substrate:	0.488
PAMPA:	1.0 ? 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):	0.999
20% Bioavailability (F20%):	0.412	30% Bioavailability (F30%):	0.984
50% Bioavailability (F50%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.707
Plasma Protein Binding (PPB):	28.229%	Volume Distribution (VD):	-0.644
Fu:	69.942% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.177	BCRP inhibitor:	0.024
BSEP inhibitor:	0.059

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.09	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.037	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.126	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.001
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):

1.256

Half-life (T1/2):

2.468

ADMET: Toxicity

hERG Blockers:	0.014	hERG Blockers (10um):	0.473
Human Hepatotoxicity (H-HT):	0.301	Drug-induced Liver Injury (DILI):	0.685
AMES Toxicity:	0.666	Rat Oral Acute Toxicity:	0.488
Maximum Recommended Daily Dose:	0.159	Skin Sensitization:	0.045
Carcinogencity:	0.12	Eye Corrosion:	0.0
Eye Irritation:	0.155	Respiratory Toxicity:	0.297
Drug-induced Neurotoxicity:	0.494	Ototoxicity:	0.983
Hematotoxicity:	0.015	Drug-induced Nephrotoxicity:	0.029
Genotoxicity:	0.177	RPMI-8226 Immunitoxicity:	0.058
A549 Cytotoxicity:	0.003	Hek293 Cytotoxicity:	0.309
BCF:	-0.144 ? 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:	0.591 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	1.324 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	0.18 ? 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
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	Seeds	n.a.		DOI[10.1002/ejlt.201100207]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	Seeds	n.a.		DOI[10.5219/332]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20121251]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22612410]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24417583]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[26923696]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38792265]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	Seed Oil	n.a.	n.a.	Database[FooDB]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12088	Conyza canadensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25114	Linum usitatissimum	Species	Linaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12088	Conyza canadensis	Species	Asteraceae	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 NPC218324 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	28741
0.1-0.2	17179
0.2-0.3	3105
0.3-0.4	694
0.4-0.5	105
0.5-0.6	25
0.6-0.7	5
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
0.7436	Intermediate Similarity	NPC143326
0.6977	Remote Similarity	NPC145112
0.6458	Remote Similarity	NPC147292
0.641	Remote Similarity	NPC323574
0.6275	Remote Similarity	NPC12040
0.6154	Remote Similarity	NPC285003
0.5882	Remote Similarity	NPC34877
0.5854	Remote Similarity	NPC124963
0.5833	Remote Similarity	NPC89145
0.5833	Remote Similarity	NPC157514
0.5833	Remote Similarity	NPC322314
0.5833	Remote Similarity	NPC269166
0.5818	Remote Similarity	NPC143446
0.5789	Remote Similarity	NPC294293
0.5714	Remote Similarity	NPC266389
0.5714	Remote Similarity	NPC122245
0.5714	Remote Similarity	NPC216605
0.5517	Remote Similarity	NPC285588
0.5517	Remote Similarity	NPC110072
0.5349	Remote Similarity	NPC326533
0.5333	Remote Similarity	NPC31496
0.5217	Remote Similarity	NPC233726
0.5208	Remote Similarity	NPC303727
0.5172	Remote Similarity	NPC250619
0.5172	Remote Similarity	NPC57751
0.5102	Remote Similarity	NPC13143
0.5102	Remote Similarity	NPC294813
0.5098	Remote Similarity	NPC219040
0.5085	Remote Similarity	NPC163812
0.5082	Remote Similarity	NPC57607
0.5082	Remote Similarity	NPC278506

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC218324 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7636
0.1-0.2	1401
0.2-0.3	90
0.3-0.4	17
0.4-0.5	5
0.5-0.6	0
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
0.6	Remote Similarity	NPD3181	Phase 3

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