NPASS Compound

Natural Product: NPC294813

Natural Product ID	NPC294813
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Hexenyl-Beta-D-Glucopyranoside
IUPAC Name	(2R,3R,4S,5S,6R)-2-[(E)-hex-3-enoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2152486
PubChem CID	5318046
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

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 40 40 0 0 0 0 0 0 0 0999 V2000 3.3339 0.8502 -2.6235 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9983 0.0025 -1.5882 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0316 -0.7086 -0.7008 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0072 -0.5236 0.6143 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0871 -1.1853 1.5539 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1237 -2.1282 0.9234 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2689 -1.6126 -0.0002 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5919 -0.6336 0.3966 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9324 -0.9960 0.3049 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6973 -0.0538 0.9909 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1533 -0.4524 1.0595 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3318 -1.6683 1.7109 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6244 1.3074 0.3294 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6486 1.2759 -0.8354 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3794 0.6019 -0.4361 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5016 1.4941 0.2026 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2842 0.6966 -1.9164 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3180 2.3197 1.2384 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6793 1.9216 -2.5720 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6077 0.5044 -3.6508 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2468 0.8454 -2.4909 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5872 -0.8060 -2.0994 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7192 0.6033 -1.0311 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3090 -1.4088 -1.1034 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7332 0.1791 1.0235 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5190 -0.3922 2.0827 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6850 -1.7593 2.3001 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6017 -2.6656 1.7640 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6918 -2.9561 0.4036 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4148 -0.4322 1.4858 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3132 0.0069 2.0261 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6714 0.3583 1.6283 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6306 -0.5060 0.0743 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2272 -1.5817 2.6886 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6088 1.5695 -0.1076 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4291 2.3283 -1.1062 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1221 0.2766 -1.3886 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2036 2.4015 -0.0575 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0695 -0.2510 -2.0214 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7320 3.1783 0.9277 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 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 10 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 14 17 1 0 13 18 1 0 15 8 1 0 1 19 1 0 1 20 1 0 1 21 1 0 2 22 1 0 2 23 1 0 3 24 1 0 4 25 1 0 5 26 1 0 5 27 1 0 6 28 1 0 6 29 1 0 8 30 1 1 10 31 1 1 11 32 1 0 11 33 1 0 12 34 1 0 13 35 1 6 14 36 1 6 15 37 1 6 16 38 1 0 17 39 1 0 18 40 1 0 M END

Standard InCHIKey	OZIPFYKAIOOVEJ-WQPBHKFLSA-N
Standard InCHI	InChI=1S/C12H22O6/c1-2-3-4-5-6-17-12-11(16)10(15)9(14)8(7-13)18-12/h3-4,8-16H,2,5-7H2,1H3/b4-3+/t8-,9-,10+,11-,12-/m1/s1
SMILES	CC/C=C/CCO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	262.14	Volume:	257.657 ? Van der Waals volume.
Dense:	1.017	LogP:	0.089 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.336 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.282 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	7.0
TPSA:	99.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	1.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.368	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.84	Fsp³:	0.833
MCE-18:	19.636 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.126	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.013 ? 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:	0.519	Promiscuous compounds:	0.006

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.358	MDCK Permeability:	-5.049
Pgp-inhibitor:	0.172	Pgp-substrate:	0.026
PAMPA:	0.206 ? 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):	0.62
20% Bioavailability (F20%):	0.539	30% Bioavailability (F30%):	0.996
50% Bioavailability (F50%):	0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.017
Plasma Protein Binding (PPB):	75.651%	Volume Distribution (VD):	-0.603
Fu:	25.753% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.997
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.086
BSEP inhibitor:	0.548

ADMET: Metabolism

CYP1A2-inhibitor:	0.133	CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.476	CYP2C19-substrate:	0.008
CYP2C9-inhibitor:	0.083	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.004	CYP2D6-substrate:	0.068
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.307
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.963
HLM stability:	0.616 ? 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):

4.102

Half-life (T1/2):

1.603

ADMET: Toxicity

hERG Blockers:	0.019	hERG Blockers (10um):	0.124
Human Hepatotoxicity (H-HT):	0.704	Drug-induced Liver Injury (DILI):	0.532
AMES Toxicity:	0.673	Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.02	Skin Sensitization:	0.996
Carcinogencity:	0.271	Eye Corrosion:	0.005
Eye Irritation:	0.584	Respiratory Toxicity:	0.066
Drug-induced Neurotoxicity:	0.031	Ototoxicity:	0.848
Hematotoxicity:	0.44	Drug-induced Nephrotoxicity:	0.459
Genotoxicity:	0.073	RPMI-8226 Immunitoxicity:	0.086
A549 Cytotoxicity:	0.187	Hek293 Cytotoxicity:	0.153
BCF:	0.378 ? 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:	2.828 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.215 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.334 ? 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
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	stems	Wulai Hsiang, Taipei County, Taiwan	2005-MAY	PMID[17253858]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23025417]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	stem bark	Laifeng, Hubei Province, China	2012-JUL	PMID[26087384]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10900	Cinnamomum subavenium	Species	Lauraceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Others	1

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
NPT2	Others	Unspecified	n.a.	IC50	>	150000.0	nM	PMID[23025417]

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 NPC294813 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	21853
0.1-0.2	23374
0.2-0.3	3766
0.3-0.4	655
0.4-0.5	187
0.5-0.6	15
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	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC13143
0.7021	Intermediate Similarity	NPC280367
0.6923	Remote Similarity	NPC233726
0.6585	Remote Similarity	NPC155457
0.6486	Remote Similarity	NPC124963
0.6279	Remote Similarity	NPC606861
0.6279	Remote Similarity	NPC607126
0.5897	Remote Similarity	NPC326533
0.5833	Remote Similarity	NPC277570
0.5676	Remote Similarity	NPC107914
0.5676	Remote Similarity	NPC242073
0.5625	Remote Similarity	NPC147292
0.5526	Remote Similarity	NPC23134
0.5263	Remote Similarity	NPC42503
0.5263	Remote Similarity	NPC282143
0.5263	Remote Similarity	NPC299781
0.5263	Remote Similarity	NPC157193
0.5263	Remote Similarity	NPC608193
0.5238	Remote Similarity	NPC143326
0.52	Remote Similarity	NPC63058
0.5116	Remote Similarity	NPC31496
0.5111	Remote Similarity	NPC268243

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC294813 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6926
0.1-0.2	2082
0.2-0.3	116
0.3-0.4	12
0.4-0.5	13
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
0.5349	Remote Similarity	NPD904	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