NPASS Compound

Natural Product: NPC534715

Natural Product ID	NPC534715
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2S)-2-(3-hydroxy-4-methoxyphenyl)-5-methoxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,3-dihydrochromen-4-one
IUPAC Name	(2~{S})-2-(3-hydroxy-4-methoxy-phenyl)-5-methoxy-7-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chroman-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 60 63 0 0 0 0 0 0 0 0999 V2000 0.6601 5.1798 1.9638 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6803 4.0019 2.3958 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7782 2.7627 2.7438 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5489 1.8552 1.9766 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6088 0.5374 2.3706 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9515 0.0360 3.4922 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8699 -1.4303 3.7042 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1454 -2.1758 3.5117 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0547 -3.0869 2.2994 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5173 -4.2353 2.2466 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3839 -2.5396 1.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8962 -2.6419 -0.0975 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0928 -3.3555 -0.2642 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6668 -3.4014 -1.6063 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2280 -2.0566 -1.1694 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0258 -1.3452 -0.9432 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5891 -0.8028 -2.0474 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4495 -0.5426 -3.3508 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5410 0.8862 -3.5495 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7566 1.3308 -3.0638 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4653 2.2570 -1.8414 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6685 2.7449 -1.4061 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7785 0.3817 -2.6218 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0814 0.9195 -2.7656 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7570 -0.9932 -3.1813 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4469 -1.8962 -2.1255 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6352 -1.0716 -4.2021 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9764 -0.1061 -5.1632 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4747 -1.3033 0.3303 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1900 -1.8749 1.4183 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1258 -1.8722 2.7356 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1983 0.9592 4.2419 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1394 2.2467 3.8591 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6304 3.1535 4.6628 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0944 5.2802 1.0527 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2030 5.9892 2.6212 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6176 5.5915 1.4823 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0734 2.1541 1.0940 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2296 -0.1093 1.7850 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5098 -1.6548 4.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9041 -1.3626 3.1990 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5175 -2.7044 4.3826 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4667 -4.1491 -1.5906 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0828 -2.3840 -1.8028 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8914 -3.7137 -2.2960 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5586 -2.0950 -2.1722 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4566 -0.8602 -3.8333 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1953 2.0308 -3.8142 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1092 1.5359 -1.0593 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7731 3.0466 -2.0638 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0426 2.2213 -0.6489 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6922 0.2630 -1.4750 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5363 0.8249 -1.9092 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6597 -1.2873 -3.7183 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8859 -1.5366 -1.2943 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4278 -1.9910 -4.6697 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2190 -0.5949 -6.0010 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4289 -0.8113 0.5486 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3201 0.5728 5.0891 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3353 3.2227 5.6393 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 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 2 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 1 0 29 30 2 0 30 31 1 0 6 32 1 0 32 33 2 0 33 34 1 0 33 3 1 0 31 7 1 0 30 11 1 0 27 18 1 0 1 35 1 0 1 36 1 0 1 37 1 0 4 38 1 0 5 39 1 0 7 40 1 1 8 41 1 0 8 42 1 0 14 43 1 0 14 44 1 0 14 45 1 0 15 46 1 0 18 47 1 6 20 48 1 6 21 49 1 0 21 50 1 0 22 51 1 0 23 52 1 1 24 53 1 0 25 54 1 6 26 55 1 0 27 56 1 6 28 57 1 0 29 58 1 0 32 59 1 0 34 60 1 0 M END

Standard InCHIKey	PKYDZNNHKUQLGS-MBTNQKKPSA-N
Standard InCHI	InChI=1S/C23H26O11/c1-30-14-4-3-10(5-12(14)25)15-8-13(26)19-16(31-2)6-11(7-17(19)33-15)32-23-22(29)21(28)20(27)18(9-24)34-23/h3-7,15,18,20-25,27-29H,8-9H2,1-2H3/t15-,18+,20+,21-,22+,23+/m0/s1
SMILES	COC1=CC=C([C@@H]2CC(=O)C3=C(OC)C=C(O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)C=C3O2)C=C1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	478.15	Volume:	450.376 ? Van der Waals volume.
Dense:	1.062	LogP:	0.884 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.389 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.973 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	24.0
TPSA:	164.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.388	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.05	Fsp³:	0.435
MCE-18:	89.03 ? 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:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.596	Fluc inhibitor:	0.298 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.284 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.559 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.085	Promiscuous compounds:	0.307

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.09	MDCK Permeability:	-5.162
Pgp-inhibitor:	0.004	Pgp-substrate:	0.005
PAMPA:	0.606 ? 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):	0.107
20% Bioavailability (F20%):	0.004	30% Bioavailability (F30%):	0.308
50% Bioavailability (F50%):	0.87

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.198
Plasma Protein Binding (PPB):	83.249%	Volume Distribution (VD):	-0.296
Fu:	15.884% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.329
BSEP inhibitor:	0.15

ADMET: Metabolism

CYP1A2-inhibitor:	0.004	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.004
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.013	CYP3A4-substrate:	0.906
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.202
HLM stability:	0.048 ? 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):

2.616

Half-life (T1/2):

4.032

ADMET: Toxicity

hERG Blockers:	0.046	hERG Blockers (10um):	0.123
Human Hepatotoxicity (H-HT):	0.86	Drug-induced Liver Injury (DILI):	0.987
AMES Toxicity:	0.945	Rat Oral Acute Toxicity:	0.087
Maximum Recommended Daily Dose:	0.104	Skin Sensitization:	0.995
Carcinogencity:	0.446	Eye Corrosion:	0.0
Eye Irritation:	0.29	Respiratory Toxicity:	0.12
Drug-induced Neurotoxicity:	0.122	Ototoxicity:	0.939
Hematotoxicity:	0.484	Drug-induced Nephrotoxicity:	0.952
Genotoxicity:	0.874	RPMI-8226 Immunitoxicity:	0.221
A549 Cytotoxicity:	0.605	Hek293 Cytotoxicity:	0.311
BCF:	0.431 ? 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:	3.074 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.741 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.861 ? 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
NPO52215	Cleome viscosa	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC534715 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	16706
0.1-0.2	27654
0.2-0.3	4397
0.3-0.4	829
0.4-0.5	237
0.5-0.6	25
0.6-0.7	7
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8143	Intermediate Similarity	NPC5778
0.7361	Intermediate Similarity	NPC206378
0.6757	Remote Similarity	NPC219163
0.6538	Remote Similarity	NPC236934
0.64	Remote Similarity	NPC97052
0.6364	Remote Similarity	NPC29830
0.6267	Remote Similarity	NPC169248
0.6267	Remote Similarity	NPC72649
0.6104	Remote Similarity	NPC39351
0.5977	Remote Similarity	NPC105095
0.5977	Remote Similarity	NPC177731
0.5977	Remote Similarity	NPC725
0.5974	Remote Similarity	NPC170475
0.5897	Remote Similarity	NPC26195
0.5862	Remote Similarity	NPC44328
0.5862	Remote Similarity	NPC79056
0.5769	Remote Similarity	NPC45400
0.5696	Remote Similarity	NPC471457
0.561	Remote Similarity	NPC477502
0.5432	Remote Similarity	NPC279298
0.5278	Remote Similarity	NPC23084
0.5256	Remote Similarity	NPC189115
0.5238	Remote Similarity	NPC472383
0.5238	Remote Similarity	NPC298847
0.5224	Remote Similarity	NPC192810
0.5211	Remote Similarity	NPC18727
0.5211	Remote Similarity	NPC599987
0.5181	Remote Similarity	NPC181014
0.5143	Remote Similarity	NPC221090
0.5143	Remote Similarity	NPC145900
0.5139	Remote Similarity	NPC218685
0.5111	Remote Similarity	NPC97285
0.5063	Remote Similarity	NPC98777
0.5056	Remote Similarity	NPC105283

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC534715 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3970
0.1-0.2	5043
0.2-0.3	120
0.3-0.4	14
0.4-0.5	2
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
0.5862	Remote Similarity	NPD7074	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