NPASS Compound

Natural Product: NPC560917

Natural Product ID	NPC560917
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-(2,4-dihydroxyphenyl)-5-hydroxy-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	3-(2,4-dihydroxyphenyl)-5-hydroxy-7-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 52 55 0 0 0 0 0 0 0 0999 V2000 3.2361 -1.3705 -0.2883 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9546 -0.1646 -0.0201 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9419 0.7711 0.2064 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3305 0.3733 0.1378 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9860 0.4563 -1.0687 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3285 0.0736 -1.1426 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9858 -0.3797 -0.0257 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3210 -0.7418 -0.1794 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3390 -0.4660 1.1842 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0158 -0.0856 1.2432 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3491 -0.1699 2.4699 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5379 2.0624 0.4920 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2665 2.3802 0.5444 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2939 1.5341 0.3383 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0275 1.8534 0.3902 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0417 0.9246 0.1648 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3441 1.3151 0.2331 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4977 0.5716 0.0474 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2592 1.0584 -1.0368 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1255 0.1103 -1.5238 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.4902 -0.9404 -2.3736 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4906 -1.8203 -2.7872 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8961 -0.4629 -0.3567 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4362 -1.7156 -0.0309 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8064 0.4956 0.8274 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1271 1.7810 0.3902 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3722 0.5425 1.3099 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0910 -0.6320 2.0336 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6900 -0.3548 -0.1190 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6508 -0.7192 -0.1807 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0112 -2.0385 -0.4733 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6273 0.2244 0.0474 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4522 0.8134 -1.9281 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8156 0.1512 -2.1085 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5600 -1.5712 -0.7056 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8835 -0.8239 2.0331 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9147 -1.0501 2.7452 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3240 2.8102 0.6731 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3082 2.8705 0.6157 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2853 -0.4735 -0.1855 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8741 0.6454 -2.1614 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7186 -1.5294 -1.8804 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0363 -0.4482 -3.2488 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0604 -2.6520 -3.0964 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9853 -0.5353 -0.5947 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9320 -2.0297 0.7815 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4940 0.1481 1.6255 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4898 1.7370 -0.5118 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1649 1.3880 1.9665 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4446 -0.4235 2.7495 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3859 -1.1390 -0.3068 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7492 -2.3541 -1.4183 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 2 0 10 11 1 0 3 12 2 0 12 13 1 0 13 14 1 0 14 15 2 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 20 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 16 29 2 0 29 30 1 0 30 31 1 0 30 32 2 0 32 2 1 0 10 4 1 0 32 14 1 0 27 18 1 0 5 33 1 0 6 34 1 0 8 35 1 0 9 36 1 0 11 37 1 0 12 38 1 0 15 39 1 0 18 40 1 6 20 41 1 6 21 42 1 0 21 43 1 0 22 44 1 0 23 45 1 6 24 46 1 0 25 47 1 1 26 48 1 0 27 49 1 1 28 50 1 0 29 51 1 0 31 52 1 0 M END

Standard InCHIKey	VYYHGKQKCBDQKO-FZHKGVQDSA-N
Standard InCHI	InChI=1S/C21H20O11/c22-6-15-18(27)19(28)20(29)21(32-15)31-9-4-13(25)16-14(5-9)30-7-11(17(16)26)10-2-1-8(23)3-12(10)24/h1-5,7,15,18-25,27-29H,6H2/t15-,18+,19-,20+,21+/m0/s1
SMILES	O=C1C(C2=CC=C(O)C=C2O)=COC2=CC(O[C@@H]3O[C@@H](CO)[C@@H](O)[C@H](O)[C@H]3O)=CC(O)=C12

Calculated Properties

Physi-Chem Properties

Molecular Weight:	448.1	Volume:	413.147 ? Van der Waals volume.
Dense:	1.085	LogP:	0.584 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.184 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.31 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	24.0
TPSA:	190.28 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	7.0	Rings:	4.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.279	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.005	Fsp³:	0.286
MCE-18:	87.63 ? 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:	0.598	Fluc inhibitor:	0.296 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.854 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.73 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.283	Promiscuous compounds:	0.533

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.434	MDCK Permeability:	-5.024
Pgp-inhibitor:	0.0	Pgp-substrate:	0.434
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):	0.224
20% Bioavailability (F20%):	0.476	30% Bioavailability (F30%):	0.958
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.41
Plasma Protein Binding (PPB):	85.83%	Volume Distribution (VD):	-0.117
Fu:	15.568% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.898
OATP1B3 inhibitor:	0.99	BCRP inhibitor:	0.524
BSEP inhibitor:	0.003

ADMET: Metabolism

CYP1A2-inhibitor:	0.04	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.092
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.006
HLM stability:	0.001 ? 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):

1.756

Half-life (T1/2):

3.698

ADMET: Toxicity

hERG Blockers:	0.019	hERG Blockers (10um):	0.229
Human Hepatotoxicity (H-HT):	0.556	Drug-induced Liver Injury (DILI):	0.878
AMES Toxicity:	0.808	Rat Oral Acute Toxicity:	0.084
Maximum Recommended Daily Dose:	0.085	Skin Sensitization:	0.948
Carcinogencity:	0.16	Eye Corrosion:	0.0
Eye Irritation:	0.66	Respiratory Toxicity:	0.041
Drug-induced Neurotoxicity:	0.003	Ototoxicity:	0.84
Hematotoxicity:	0.062	Drug-induced Nephrotoxicity:	0.528
Genotoxicity:	0.972	RPMI-8226 Immunitoxicity:	0.108
A549 Cytotoxicity:	0.271	Hek293 Cytotoxicity:	0.38
BCF:	0.455 ? 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:	2.995 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.356 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.604 ? 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
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24342	Lupinus albus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24342	Lupinus albus	Species	Fabaceae	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 NPC560917 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	24083
0.1-0.2	22274
0.2-0.3	2403
0.3-0.4	789
0.4-0.5	225
0.5-0.6	46
0.6-0.7	19
0.7-0.8	0
0.8-0.85	4
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	NPC80140
0.8472	Intermediate Similarity	NPC234739
0.8375	Intermediate Similarity	NPC479403
0.8219	Intermediate Similarity	NPC197896
0.8219	Intermediate Similarity	NPC313163
0.7468	Intermediate Similarity	NPC479406
0.7308	Intermediate Similarity	NPC138540
0.7179	Intermediate Similarity	NPC73511
0.6941	Remote Similarity	NPC479405
0.6923	Remote Similarity	NPC348541
0.686	Remote Similarity	NPC479404
0.662	Remote Similarity	NPC90665
0.6585	Remote Similarity	NPC307938
0.642	Remote Similarity	NPC156457
0.6386	Remote Similarity	NPC479402
0.6375	Remote Similarity	NPC160515
0.6265	Remote Similarity	NPC205076
0.622	Remote Similarity	NPC161749
0.619	Remote Similarity	NPC479401
0.6098	Remote Similarity	NPC39360
0.6098	Remote Similarity	NPC29763
0.6098	Remote Similarity	NPC210003
0.6071	Remote Similarity	NPC100720
0.6024	Remote Similarity	NPC297987
0.6024	Remote Similarity	NPC323593
0.6024	Remote Similarity	NPC203500
0.6	Remote Similarity	NPC303913
0.5833	Remote Similarity	NPC105511
0.5823	Remote Similarity	NPC191154
0.5814	Remote Similarity	NPC481043
0.5714	Remote Similarity	NPC289667
0.5714	Remote Similarity	NPC261866
0.5682	Remote Similarity	NPC116458
0.5682	Remote Similarity	NPC246943
0.5667	Remote Similarity	NPC487212
0.5647	Remote Similarity	NPC95090
0.5647	Remote Similarity	NPC258035
0.5647	Remote Similarity	NPC277205
0.5647	Remote Similarity	NPC27408
0.5647	Remote Similarity	NPC37919
0.5647	Remote Similarity	NPC136042
0.5647	Remote Similarity	NPC189142
0.5647	Remote Similarity	NPC77660
0.5632	Remote Similarity	NPC224462
0.5618	Remote Similarity	NPC48773
0.5581	Remote Similarity	NPC84362
0.5568	Remote Similarity	NPC610187
0.5556	Remote Similarity	NPC134819
0.5506	Remote Similarity	NPC307518
0.5455	Remote Similarity	NPC285197
0.5444	Remote Similarity	NPC479407
0.5412	Remote Similarity	NPC45165
0.5393	Remote Similarity	NPC22832
0.5393	Remote Similarity	NPC243930
0.5393	Remote Similarity	NPC229729
0.5393	Remote Similarity	NPC601144
0.5368	Remote Similarity	NPC64425
0.5333	Remote Similarity	NPC311830
0.5333	Remote Similarity	NPC605784
0.5244	Remote Similarity	NPC78697
0.5233	Remote Similarity	NPC135345
0.5222	Remote Similarity	NPC486578
0.5172	Remote Similarity	NPC211014
0.5165	Remote Similarity	NPC607707
0.5161	Remote Similarity	NPC251417
0.5132	Remote Similarity	NPC303644
0.5114	Remote Similarity	NPC487213
0.5109	Remote Similarity	NPC601586
0.5102	Remote Similarity	NPC35119
0.5057	Remote Similarity	NPC331652
0.5056	Remote Similarity	NPC22195
0.5056	Remote Similarity	NPC21190
0.5055	Remote Similarity	NPC601607

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC560917 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5768
0.1-0.2	3315
0.2-0.3	55
0.3-0.4	8
0.4-0.5	3
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
0.622	Remote Similarity	NPD4381	Clinical (unspecified phase)

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