Natural Product: NPC553999

Natural Product IDNPC553999
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2~{S},3~{S})-2-(2,5-dihydroxyphenyl)chromane-3,5,7-triol
IUPAC Name (2~{S},3~{S})-2-(2,5-dihydroxyphenyl)chromane-3,5,7-triol
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

Standard InCHIKey INFSVMACOKVKOV-ZFWWWQNUSA-N
Standard InCHI InChI=1S/C15H14O6/c16-7-1-2-11(18)10(3-7)15-13(20)6-9-12(19)4-8(17)5-14(9)21-15/h1-5,13,15-20H,6H2/t13-,15-/m0/s1
SMILES OC1=CC(O)=C2C[C@H](O)[C@H](C3=CC(O)=CC=C3O)OC2=C1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.08 Volume:   279.249
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Van der Waals volume.
Dense:   1.039 LogP:   0.594
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.04
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.242
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   110.38
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Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.51 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.411 Fsp3:   0.2
MCE-18:   60.0
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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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.561 Fluc inhibitor:   0.481
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.276
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.044
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.465 Promiscuous compounds:   0.265

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.989 MDCK Permeability:   -4.897
Pgp-inhibitor:   0.002 Pgp-substrate:   0.129
PAMPA:   0.891
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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):   0.001
20% Bioavailability (F20%):   0.582 30% Bioavailability (F30%):   0.875
50% Bioavailability (F50%):   0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.884
Plasma Protein Binding (PPB):   86.759% Volume Distribution (VD):   0.281
Fu: 18.636%
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The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.706
OATP1B3 inhibitor:   0.646 BCRP inhibitor:   0.01
BSEP inhibitor:   0.702

ADMET: Metabolism

CYP1A2-inhibitor:   0.978 CYP1A2-substrate:   0.019
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.016
CYP2C9-inhibitor:   0.983 CYP2C9-substrate:   0.014
CYP2D6-inhibitor:   0.995 CYP2D6-substrate:   0.555
CYP3A4-inhibitor:   0.184 CYP3A4-substrate:   0.972
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.686
HLM stability:   0.162
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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):  13.837 Half-life (T1/2):  2.376

ADMET: Toxicity

hERG Blockers:  0.061 hERG Blockers (10um):  0.602
Human Hepatotoxicity (H-HT):  0.686 Drug-induced Liver Injury (DILI):  0.051
AMES Toxicity:  0.626 Rat Oral Acute Toxicity:  0.467
Maximum Recommended Daily Dose:  0.802 Skin Sensitization:  0.683
Carcinogencity:  0.328 Eye Corrosion:  0.016
Eye Irritation:  0.993 Respiratory Toxicity:  0.813
Drug-induced Neurotoxicity:  0.088 Ototoxicity:  0.545
Hematotoxicity:  0.045 Drug-induced Nephrotoxicity:  0.227
Genotoxicity:  0.9 RPMI-8226 Immunitoxicity:  0.088
A549 Cytotoxicity:  0.43 Hek293 Cytotoxicity:  0.77
BCF:   1.094
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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:   3.166
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.293
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.76
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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
NPO10677 Prunus prostrata Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10677 Prunus prostrata Species Rosaceae 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
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 NPC553999 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7083 Intermediate Similarity NPC207179
0.7083 Intermediate Similarity NPC167571
0.7083 Intermediate Similarity NPC278552
0.68 Remote Similarity NPC261619
0.68 Remote Similarity NPC61477
0.68 Remote Similarity NPC78770
0.68 Remote Similarity NPC219876
0.68 Remote Similarity NPC126029
0.68 Remote Similarity NPC15658
0.6735 Remote Similarity NPC268266
0.6735 Remote Similarity NPC42760
0.6735 Remote Similarity NPC220825
0.6735 Remote Similarity NPC268342
0.6471 Remote Similarity NPC47398
0.6471 Remote Similarity NPC234333
0.6471 Remote Similarity NPC260898
0.6226 Remote Similarity NPC606962
0.6182 Remote Similarity NPC16435
0.6182 Remote Similarity NPC171932
0.6111 Remote Similarity NPC61946
0.5156 Remote Similarity NPC9636
0.5156 Remote Similarity NPC607430
0.5152 Remote Similarity NPC308402
0.5152 Remote Similarity NPC28440

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC553999 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.68 Remote Similarity NPD1612 Clinical (unspecified phase)
0.68 Remote Similarity NPD1613 Phase 4

Bioactivity similarity

  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