NPASS Compound

Natural Product: NPC282409

Natural Product ID	NPC282409
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	2-(3,4-Dihydroxy-5-Hydroxymethyl-Tetrahydro-Furan-2-Yloxymethyl)-6-[(S)-3-(4-Hydroxy-Phenyl)-1-Methyl-Propoxy]-Tetrahydro-Pyran-3,4,5-Triol
IUPAC Name	(2R,3S,4S,5R,6R)-2-[[(2R,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxymethyl]-6-[(2S)-4-(4-hydroxyphenyl)butan-2-yl]oxyoxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL612191
PubChem CID	38347392
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 64 66 0 0 0 0 0 0 0 0999 V2000 3.1078 -0.0486 -0.9780 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5214 -0.7937 0.1742 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8670 -0.1909 1.4804 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2693 -0.1143 1.9151 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1471 0.6706 1.0527 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1785 2.0595 1.2279 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0178 2.8322 0.4879 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8563 2.2560 -0.4525 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8281 0.9024 -0.6256 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9933 0.1303 0.1099 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7026 3.0666 -1.1941 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1293 -0.8497 0.1151 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5914 -2.1021 0.1250 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2522 -2.4267 1.3165 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5497 -1.6177 1.1498 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1708 -2.1165 -0.1208 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2863 -1.9375 -1.2931 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2372 -0.5290 -1.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3527 0.0689 -2.1404 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3875 0.4836 -1.4685 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7260 1.9862 -1.7034 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0146 2.0047 -0.8653 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6214 0.6910 -1.3261 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4518 0.0267 -0.2695 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4334 0.9080 0.1801 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6240 -0.0870 -1.8400 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7945 3.0964 -1.1254 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7523 2.8065 -1.1985 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0036 -2.3473 -1.0849 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2986 -3.5531 0.0157 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2089 -0.2899 1.0372 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6158 -3.7659 1.3215 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2706 0.1436 -1.7510 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8819 -0.5859 -1.5487 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4573 0.9739 -0.7665 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9403 -1.8567 0.2270 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3210 -0.8383 2.2634 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3472 0.8182 1.5658 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3604 0.3670 2.9496 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7165 -1.1564 2.0587 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5155 2.4919 1.9681 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0657 3.9038 0.5983 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4848 0.4368 -1.3646 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9660 -0.9559 -0.0241 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7011 3.0226 -1.0499 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4728 -2.8202 0.1818 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1902 -2.1863 2.2748 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2427 -1.8164 1.9909 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2099 -1.8066 -0.2214 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6633 -2.6026 -2.1655 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5483 0.0955 -1.1447 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5800 -0.5709 -2.7629 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3307 0.3844 -0.3869 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0278 2.1625 -2.7343 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6648 1.9283 0.1938 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3044 0.9693 -2.1819 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9521 -0.8414 -0.7485 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8438 -0.3599 0.5570 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1853 0.9887 -0.4603 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2087 3.3792 -0.2534 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9739 2.9930 -0.2383 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7286 -3.8054 -0.8473 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8392 0.2474 1.5898 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1759 -4.3233 1.1629 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 8 11 1 0 2 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 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 23 26 1 0 22 27 1 0 21 28 1 0 17 29 1 0 16 30 1 0 15 31 1 0 14 32 1 0 10 5 1 0 29 13 1 0 26 20 1 0 1 33 1 0 1 34 1 0 1 35 1 0 2 36 1 1 3 37 1 0 3 38 1 0 4 39 1 0 4 40 1 0 6 41 1 0 7 42 1 0 9 43 1 0 10 44 1 0 11 45 1 0 13 46 1 1 14 47 1 1 15 48 1 1 16 49 1 6 17 50 1 6 18 51 1 0 18 52 1 0 20 53 1 1 21 54 1 6 22 55 1 1 23 56 1 6 24 57 1 0 24 58 1 0 25 59 1 0 27 60 1 0 28 61 1 0 30 62 1 0 31 63 1 0 32 64 1 0 M END

Standard InCHIKey	DJDISCKFJXDADJ-IMNWWGSQSA-N
Standard InCHI	InChI=1S/C21H32O11/c1-10(2-3-11-4-6-12(23)7-5-11)30-21-19(28)17(26)16(25)14(32-21)9-29-20-18(27)15(24)13(8-22)31-20/h4-7,10,13-28H,2-3,8-9H2,1H3/t10-,13-,14+,15-,16+,17-,18+,19+,20+,21+/m0/s1
SMILES	C[C@@H](CCc1ccc(cc1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO)O2)O)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	460.19	Volume:	434.886 ? Van der Waals volume.
Dense:	1.058	LogP:	-0.223 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.499 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.637 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	17.0
TPSA:	178.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	7.0	Rings:	3.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.217	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.341	Fsp³:	0.714
MCE-18:	73.5 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.447	Fluc inhibitor:	0.024 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.075 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.062 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.289	Promiscuous compounds:	0.261

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.617	MDCK Permeability:	-5.015
Pgp-inhibitor:	0.0	Pgp-substrate:	0.841
PAMPA:	0.983 ? 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):	0.162
20% Bioavailability (F20%):	0.083	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.011
Plasma Protein Binding (PPB):	57.149%	Volume Distribution (VD):	-0.426
Fu:	42.514% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.056
BSEP inhibitor:	0.027

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.003
CYP3A4-inhibitor:	0.099	CYP3A4-substrate:	0.091
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.445
HLM stability:	0.071 ? 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):

2.321

Half-life (T1/2):

2.418

ADMET: Toxicity

hERG Blockers:	0.038	hERG Blockers (10um):	0.229
Human Hepatotoxicity (H-HT):	0.419	Drug-induced Liver Injury (DILI):	0.251
AMES Toxicity:	0.901	Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.01	Skin Sensitization:	0.996
Carcinogencity:	0.04	Eye Corrosion:	0.0
Eye Irritation:	0.193	Respiratory Toxicity:	0.004
Drug-induced Neurotoxicity:	0.009	Ototoxicity:	0.949
Hematotoxicity:	0.183	Drug-induced Nephrotoxicity:	0.561
Genotoxicity:	0.016	RPMI-8226 Immunitoxicity:	0.118
A549 Cytotoxicity:	0.551	Hek293 Cytotoxicity:	0.43
BCF:	0.42 ? 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:	3.126 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.636 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.631 ? 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
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	floral spikes	n.a.	n.a.	PMID[17346076]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	bark	n.a.	n.a.	PMID[9873651]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4138.1	Betula platyphylla var. japonica	Varieties	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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
Inhibition	5

Activity Type	# Activity
Organism	5

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
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	10.1	%	PMID[15497938]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	3.6	%	DrugMatrix in vitro pharmacology data
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	9.6	%	PMID[24035096]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	5.4	%	PMID[13678412]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Inhibition	=	4.0	%	PMID[18955522]

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 NPC282409 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	12473
0.1-0.2	31314
0.2-0.3	5115
0.3-0.4	802
0.4-0.5	124
0.5-0.6	7
0.6-0.7	12
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	NPC469702
0.7903	Intermediate Similarity	NPC471066
0.7778	Intermediate Similarity	NPC471067
0.7742	Intermediate Similarity	NPC476448
0.7742	Intermediate Similarity	NPC469548
0.7742	Intermediate Similarity	NPC476445
0.7455	Intermediate Similarity	NPC148055
0.6389	Remote Similarity	NPC469549
0.6324	Remote Similarity	NPC471095
0.6286	Remote Similarity	NPC164172
0.6111	Remote Similarity	NPC232454
0.6111	Remote Similarity	NPC470907
0.6111	Remote Similarity	NPC178449
0.6094	Remote Similarity	NPC160854
0.6094	Remote Similarity	NPC17968
0.6094	Remote Similarity	NPC469705
0.6094	Remote Similarity	NPC469704
0.6094	Remote Similarity	NPC469703
0.6066	Remote Similarity	NPC602133
0.5846	Remote Similarity	NPC201402
0.5574	Remote Similarity	NPC157338
0.5571	Remote Similarity	NPC79715
0.5571	Remote Similarity	NPC108659
0.5455	Remote Similarity	NPC158673
0.5224	Remote Similarity	NPC57751
0.5132	Remote Similarity	NPC199459

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC282409 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4056
0.1-0.2	4881
0.2-0.3	205
0.3-0.4	7
0.4-0.5	1
0.5-0.6	0
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
		NPD

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