NPASS Compound

Natural Product: NPC202700

Natural Product ID	NPC202700
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Beta-D-Glucopyranosyl 4-O-Beta-D-Glucopyranosylcaffeate
IUPAC Name	[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (E)-3-[3-hydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-enoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL482033
PubChem CID	11191325
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0003002] Hydroxycinnamic acid esters [CHEMONTID:0003003] Hydroxycinnamic acid 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 63 65 0 0 0 0 0 0 0 0999 V2000 9.1553 2.2369 -0.2919 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8390 1.9197 -0.0526 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3639 0.7018 -0.8127 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0264 0.4982 -0.4798 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5625 -0.7268 -0.9905 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1871 -0.7763 -0.6539 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6383 -1.7662 0.1415 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4042 -2.6594 0.5800 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1982 -1.7866 0.4752 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3865 -0.8608 0.0227 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0394 -0.8046 0.3020 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6765 -1.7198 1.0785 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0260 -1.6431 1.3294 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8264 -0.6233 0.8045 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1769 0.2973 0.0213 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8061 0.2082 -0.2260 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9047 1.3442 -0.5388 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1415 -0.6573 1.1248 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2304 0.1280 0.8230 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7348 0.6283 2.0355 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9571 1.2712 1.8670 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.3431 1.8306 3.2217 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3655 2.7257 3.6461 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0422 0.3423 1.4158 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.4143 -1.0122 1.1294 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2722 -0.7874 0.1714 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.7555 -0.1418 -0.9592 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9825 -1.5198 2.3498 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7325 0.7703 0.3041 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6874 -0.8064 -2.4864 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0465 -0.4018 -2.9564 C 0 0 2 0 0 0 0 0 0 0 0 0 7.4151 0.9137 -2.3063 C 0 0 2 0 0 0 0 0 0 0 0 0 8.6655 1.3661 -2.7243 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9975 -0.2530 -4.3627 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3820 -2.1137 -2.8642 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7279 1.4699 -0.5420 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6695 1.7367 1.0307 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2116 2.7833 -0.3535 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0030 -0.1477 -0.5382 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1212 -1.5776 -0.5430 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8244 -2.5673 1.0915 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8627 -0.0947 -0.6079 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1453 -2.5571 1.5379 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5116 -2.3908 1.9557 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3447 0.9687 -0.8568 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5565 1.7493 -1.4004 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9770 0.9616 0.1483 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9048 2.1123 1.1648 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3650 2.2746 3.2230 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3825 1.0028 3.9878 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6581 2.8306 2.9614 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7891 0.1690 2.2319 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1729 -1.6575 0.6889 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8311 -1.7495 -0.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2475 -0.7771 -1.5512 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4457 -2.3294 2.2664 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4116 1.6369 -0.0381 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9396 -0.1207 -2.9296 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7565 -1.1973 -2.6972 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6478 1.6701 -2.5605 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8229 1.0692 -3.6538 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0018 0.7389 -4.5437 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6267 -2.1297 -3.4960 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 7 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 15 17 1 0 14 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 25 28 1 0 24 29 1 0 5 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 31 34 1 0 30 35 1 0 32 3 1 0 16 11 1 0 26 19 1 0 1 36 1 0 2 37 1 0 2 38 1 0 3 39 1 6 5 40 1 1 9 41 1 0 10 42 1 0 12 43 1 0 13 44 1 0 16 45 1 0 17 46 1 0 19 47 1 6 21 48 1 6 22 49 1 0 22 50 1 0 23 51 1 0 24 52 1 1 25 53 1 6 26 54 1 6 27 55 1 0 28 56 1 0 29 57 1 0 30 58 1 6 31 59 1 6 32 60 1 1 33 61 1 0 34 62 1 0 35 63 1 0 M END

Standard InCHIKey	NCWAFVQNRSHJMH-CQGBVQOQSA-N
Standard InCHI	InChI=1S/C21H28O14/c22-6-11-14(26)16(28)18(30)20(33-11)32-10-3-1-8(5-9(10)24)2-4-13(25)35-21-19(31)17(29)15(27)12(7-23)34-21/h1-5,11-12,14-24,26-31H,6-7H2/b4-2+/t11-,12-,14-,15-,16+,17+,18-,19-,20-,21+/m1/s1
SMILES	OC[C@H]1O[C@@H](OC(=O)/C=C/c2ccc(c(c2)O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	504.15	Volume:	455.984 ? Van der Waals volume.
Dense:	1.106	LogP:	-0.792 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.262 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.616 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	20.0
TPSA:	236.06 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	9.0	Rings:	3.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.127	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.471	Fsp³:	0.571
MCE-18:	82.939 ? 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:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.759	Fluc inhibitor:	0.642 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.227 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.27 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.463	Promiscuous compounds:	0.365

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.761	MDCK Permeability:	-5.01
Pgp-inhibitor:	0.0	Pgp-substrate:	0.148
PAMPA:	0.999 ? 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):	0.994
20% Bioavailability (F20%):	0.825	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.001
Plasma Protein Binding (PPB):	56.432%	Volume Distribution (VD):	-0.382
Fu:	43.24% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.004
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	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:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.003
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.82
HLM stability:	0.002 ? 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):

1.293

Half-life (T1/2):

4.165

ADMET: Toxicity

hERG Blockers:	0.004	hERG Blockers (10um):	0.024
Human Hepatotoxicity (H-HT):	0.723	Drug-induced Liver Injury (DILI):	0.943
AMES Toxicity:	0.98	Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.002	Skin Sensitization:	1.0
Carcinogencity:	0.105	Eye Corrosion:	0.0
Eye Irritation:	0.02	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.001	Ototoxicity:	0.992
Hematotoxicity:	0.288	Drug-induced Nephrotoxicity:	0.953
Genotoxicity:	0.312	RPMI-8226 Immunitoxicity:	0.137
A549 Cytotoxicity:	0.272	Hek293 Cytotoxicity:	0.096
BCF:	0.283 ? 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:	2.749 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.495 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.473 ? 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
NPO14305	Moricandia arvensis	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844940]
NPO14305	Moricandia arvensis	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14305	Moricandia arvensis	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

Activity Type	# Activity
Activity	1
IC50	1

Activity Type	# Activity
Non-molecular	2

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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	1.06	mM	PMID[15844940]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	95.9	ug.mL-1	PMID[15844940]

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 NPC202700 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	14540
0.1-0.2	29415
0.2-0.3	4301
0.3-0.4	1190
0.4-0.5	352
0.5-0.6	36
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	0

Similarity Score	Similarity Level	Natural Product ID
0.8596	High Similarity	NPC100389
0.7895	Intermediate Similarity	NPC481303
0.7681	Intermediate Similarity	NPC476864
0.7571	Intermediate Similarity	NPC476866
0.726	Intermediate Similarity	NPC476865
0.6949	Remote Similarity	NPC232880
0.6825	Remote Similarity	NPC157554
0.6667	Remote Similarity	NPC59324
0.6615	Remote Similarity	NPC186418
0.6575	Remote Similarity	NPC476867
0.6557	Remote Similarity	NPC604356
0.6533	Remote Similarity	NPC476868
0.65	Remote Similarity	NPC11724
0.629	Remote Similarity	NPC19470
0.6184	Remote Similarity	NPC476869
0.6143	Remote Similarity	NPC186406
0.6119	Remote Similarity	NPC185778
0.6111	Remote Similarity	NPC310064
0.6027	Remote Similarity	NPC232228
0.5972	Remote Similarity	NPC488085
0.5738	Remote Similarity	NPC200092
0.5733	Remote Similarity	NPC292443
0.5714	Remote Similarity	NPC98777
0.5667	Remote Similarity	NPC9248
0.56	Remote Similarity	NPC145319
0.5479	Remote Similarity	NPC88043
0.5455	Remote Similarity	NPC26080
0.5455	Remote Similarity	NPC210015
0.5455	Remote Similarity	NPC165686
0.5395	Remote Similarity	NPC166180
0.5316	Remote Similarity	NPC199928
0.5303	Remote Similarity	NPC205054
0.5286	Remote Similarity	NPC65530
0.5278	Remote Similarity	NPC106944
0.52	Remote Similarity	NPC191046
0.5176	Remote Similarity	NPC89693
0.5147	Remote Similarity	NPC248355
0.5147	Remote Similarity	NPC105827
0.5143	Remote Similarity	NPC52097
0.5143	Remote Similarity	NPC307110
0.5135	Remote Similarity	NPC116229
0.5135	Remote Similarity	NPC477294
0.5135	Remote Similarity	NPC477293
0.5135	Remote Similarity	NPC606353
0.5132	Remote Similarity	NPC72249
0.5082	Remote Similarity	NPC484157
0.5079	Remote Similarity	NPC60589
0.5079	Remote Similarity	NPC469708
0.5075	Remote Similarity	NPC251102
0.5075	Remote Similarity	NPC210298
0.5072	Remote Similarity	NPC55040
0.5072	Remote Similarity	NPC25292
0.507	Remote Similarity	NPC294166
0.507	Remote Similarity	NPC115022
0.5065	Remote Similarity	NPC297342

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC202700 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4473
0.1-0.2	4531
0.2-0.3	122
0.3-0.4	22
0.4-0.5	2
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