NPASS Compound

Natural Product: NPC560224

Natural Product ID	NPC560224
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	4-[(2~{S},3~{R})-2-(hydroxymethyl)-6-(3-hydroxypropyl)-2,3-dihydro-1,4-benzodioxin-3-yl]-2-methoxy-phenol
IUPAC Name	4-[(2~{S},3~{R})-2-(hydroxymethyl)-6-(3-hydroxypropyl)-2,3-dihydro-1,4-benzodioxin-3-yl]-2-methoxy-phenol
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 47 49 0 0 0 0 0 0 0 0999 V2000 -3.3841 -3.4670 0.4338 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4079 -2.6190 -0.0488 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2365 -1.2541 -0.1541 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0628 -0.6385 0.2032 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8705 0.7446 0.1034 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5643 1.2339 0.5324 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5710 0.3100 0.0470 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7324 0.6025 0.4368 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7052 -0.3891 0.4870 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9992 -0.1116 0.8715 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0169 -1.1965 0.9146 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7214 -1.3070 -0.4325 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7355 -2.4416 -0.2733 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3978 -2.5658 -1.4956 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2960 1.1921 1.2064 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3255 2.1737 1.1548 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0268 1.9049 0.7708 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0448 2.9124 0.7214 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2203 2.6325 0.0984 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0974 2.8087 -1.3799 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7239 4.1362 -1.6398 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8955 1.4991 -0.3679 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0797 0.8970 -0.7308 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2624 -0.4724 -0.6293 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4791 -1.0665 -1.0052 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5828 -3.5470 -0.3023 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8074 -4.4807 0.5853 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0010 -3.0372 1.3989 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2528 -1.2774 0.5810 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5184 1.2169 1.6405 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4619 -1.4029 0.2234 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4943 -2.1524 1.0764 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7410 -1.0792 1.7375 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1953 -0.3499 -0.6629 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0262 -1.5916 -1.2285 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1411 -3.3527 -0.0366 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4229 -2.1833 0.5488 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3719 -2.5075 -1.2949 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3070 1.4123 1.5075 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6250 3.1821 1.4316 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9643 3.3209 0.5274 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9423 2.4945 -1.9825 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2024 2.2066 -1.7216 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2342 4.5313 -0.8699 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7410 2.5703 -0.4377 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8898 1.5042 -1.1048 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7962 -0.9960 -1.9526 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 2 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 10 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 5 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 24 3 1 0 19 6 1 0 17 8 1 0 1 26 1 0 1 27 1 0 1 28 1 0 4 29 1 0 6 30 1 1 9 31 1 0 11 32 1 0 11 33 1 0 12 34 1 0 12 35 1 0 13 36 1 0 13 37 1 0 14 38 1 0 15 39 1 0 16 40 1 0 19 41 1 1 20 42 1 0 20 43 1 0 21 44 1 0 22 45 1 0 23 46 1 0 25 47 1 0 M END

Standard InCHIKey	VSJGYMSTWHUFMX-RBUKOAKNSA-N
Standard InCHI	InChI=1S/C19H22O6/c1-23-16-10-13(5-6-14(16)22)19-18(11-21)24-15-7-4-12(3-2-8-20)9-17(15)25-19/h4-7,9-10,18-22H,2-3,8,11H2,1H3/t18-,19+/m0/s1
SMILES	COC1=CC([C@H]2OC3=CC(CCCO)=CC=C3O[C@H]2CO)=CC=C1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	346.14	Volume:	348.433 ? Van der Waals volume.
Dense:	0.993	LogP:	1.979 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.164 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.286 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	17.0
TPSA:	88.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	3.0	Rings:	3.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.743	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.104	Fsp³:	0.368
MCE-18:	53.615 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.462	Fluc inhibitor:	0.795 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.037 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.192 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.115	Promiscuous compounds:	0.285

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.334	MDCK Permeability:	-4.874
Pgp-inhibitor:	0.973	Pgp-substrate:	0.302
PAMPA:	0.076 ? 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):	0.002
20% Bioavailability (F20%):	0.05	30% Bioavailability (F30%):	0.224
50% Bioavailability (F50%):	0.894

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008	MRP1:	0.705
Plasma Protein Binding (PPB):	86.069%	Volume Distribution (VD):	-0.239
Fu:	14.925% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.992	BCRP inhibitor:	0.763
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.957	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.812	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.99	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.653	CYP2D6-substrate:	0.272
CYP3A4-inhibitor:	0.9	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.552
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):

6.488

Half-life (T1/2):

1.469

ADMET: Toxicity

hERG Blockers:	0.143	hERG Blockers (10um):	0.457
Human Hepatotoxicity (H-HT):	0.753	Drug-induced Liver Injury (DILI):	0.146
AMES Toxicity:	0.531	Rat Oral Acute Toxicity:	0.092
Maximum Recommended Daily Dose:	0.042	Skin Sensitization:	0.886
Carcinogencity:	0.321	Eye Corrosion:	0.026
Eye Irritation:	0.95	Respiratory Toxicity:	0.154
Drug-induced Neurotoxicity:	0.155	Ototoxicity:	0.704
Hematotoxicity:	0.308	Drug-induced Nephrotoxicity:	0.713
Genotoxicity:	0.039	RPMI-8226 Immunitoxicity:	0.039
A549 Cytotoxicity:	0.166	Hek293 Cytotoxicity:	0.286
BCF:	0.554 ? 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:	2.999 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.563 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.679 ? 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
NPO46902	Lamiaceae	Family	Lamiaceae	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 NPC560224 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	19411
0.1-0.2	24858
0.2-0.3	4776
0.3-0.4	640
0.4-0.5	143
0.5-0.6	24
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC5851
0.9434	High Similarity	NPC86030
0.7759	Intermediate Similarity	NPC605857
0.6667	Remote Similarity	NPC481838
0.65	Remote Similarity	NPC194519
0.629	Remote Similarity	NPC111247
0.629	Remote Similarity	NPC292056
0.5909	Remote Similarity	NPC476394
0.5882	Remote Similarity	NPC126206
0.5821	Remote Similarity	NPC98809
0.5758	Remote Similarity	NPC224876
0.5753	Remote Similarity	NPC36916
0.5753	Remote Similarity	NPC36
0.5753	Remote Similarity	NPC7154
0.5753	Remote Similarity	NPC125039
0.5753	Remote Similarity	NPC7688
0.5467	Remote Similarity	NPC138688
0.5467	Remote Similarity	NPC72787
0.5467	Remote Similarity	NPC217795
0.5467	Remote Similarity	NPC58223
0.5455	Remote Similarity	NPC29799
0.5455	Remote Similarity	NPC263367
0.5455	Remote Similarity	NPC54743
0.5316	Remote Similarity	NPC470935
0.5312	Remote Similarity	NPC293701
0.5303	Remote Similarity	NPC163332
0.5303	Remote Similarity	NPC83375
0.5254	Remote Similarity	NPC71090
0.5231	Remote Similarity	NPC16208
0.5135	Remote Similarity	NPC476347
0.5094	Remote Similarity	NPC137685

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC560224 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3856
0.1-0.2	5023
0.2-0.3	263
0.3-0.4	4
0.4-0.5	1
0.5-0.6	3
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
0.5753	Remote Similarity	NPD6166	Phase 2
0.5753	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.5753	Remote Similarity	NPD6168	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