Natural Product: NPC323467

Natural Product IDNPC323467
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VADSVXSGIFBZLI-IWQYDBTJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 18343460
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 VADSVXSGIFBZLI-IWQYDBTJSA-N
Standard InCHI InChI=1S/C16H22O7/c1-3-4-9-5-6-10(11(7-9)21-2)22-16-15(20)14(19)13(18)12(8-17)23-16/h3,5-7,12-20H,1,4,8H2,2H3/t12-,13-,14+,15-,16?/m1/s1
SMILES COC1=C(C=CC(=C1)CC=C)OC2C(C(C(C(O2)CO)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   326.14 Volume:   319.165
?
Van der Waals volume.
Dense:   1.022 LogP:   0.171
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.459
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.46
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   13.0
TPSA:   108.61
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.527 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.552 Fsp3:   0.5
MCE-18:   47.833
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.027 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.021
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.144
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.259 Promiscuous compounds:   0.009

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.591 MDCK Permeability:   -5.005
Pgp-inhibitor:   0.002 Pgp-substrate:   0.019
PAMPA:   0.569
?
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):   0.946
20% Bioavailability (F20%):   0.957 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.062 MRP1:   0.284
Plasma Protein Binding (PPB):   71.635% Volume Distribution (VD):   -0.206
Fu: 27.39%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.338
OATP1B3 inhibitor:   0.953 BCRP inhibitor:   0.677
BSEP inhibitor:   0.844

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.275 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.612 CYP2D6-substrate:   0.073
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.055
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
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):  3.264 Half-life (T1/2):  2.121

ADMET: Toxicity

hERG Blockers:  0.061 hERG Blockers (10um):  0.48
Human Hepatotoxicity (H-HT):  0.4 Drug-induced Liver Injury (DILI):  0.466
AMES Toxicity:  0.518 Rat Oral Acute Toxicity:  0.245
Maximum Recommended Daily Dose:  0.111 Skin Sensitization:  0.666
Carcinogencity:  0.345 Eye Corrosion:  0.001
Eye Irritation:  0.453 Respiratory Toxicity:  0.216
Drug-induced Neurotoxicity:  0.459 Ototoxicity:  0.814
Hematotoxicity:  0.085 Drug-induced Nephrotoxicity:  0.1
Genotoxicity:  0.043 RPMI-8226 Immunitoxicity:  0.058
A549 Cytotoxicity:  0.053 Hek293 Cytotoxicity:  0.286
BCF:   0.404
?
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:   2.991
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.635
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.636
?
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
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. aerial part n.a. PMID[15577228]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. PMID[22085682]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume 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 NPC323467 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
1.0 High Similarity NPC270849
0.9167 High Similarity NPC9912
0.8431 Intermediate Similarity NPC472024
0.7925 Intermediate Similarity NPC26653
0.7925 Intermediate Similarity NPC80600
0.76 Intermediate Similarity NPC60589
0.76 Intermediate Similarity NPC469708
0.717 Intermediate Similarity NPC166040
0.6842 Remote Similarity NPC248355
0.6786 Remote Similarity NPC19470
0.6724 Remote Similarity NPC55040
0.661 Remote Similarity NPC302378
0.6515 Remote Similarity NPC227902
0.6462 Remote Similarity NPC158635
0.6462 Remote Similarity NPC229882
0.6379 Remote Similarity NPC210015
0.6364 Remote Similarity NPC69513
0.6327 Remote Similarity NPC228907
0.629 Remote Similarity NPC37468
0.629 Remote Similarity NPC604095
0.6176 Remote Similarity NPC471063
0.614 Remote Similarity NPC215833
0.6129 Remote Similarity NPC276753
0.6129 Remote Similarity NPC205796
0.6119 Remote Similarity NPC61594
0.6111 Remote Similarity NPC25817
0.6094 Remote Similarity NPC210192
0.6032 Remote Similarity NPC246947
0.6029 Remote Similarity NPC56735
0.6 Remote Similarity NPC479029
0.5972 Remote Similarity NPC245615
0.5753 Remote Similarity NPC299706
0.5753 Remote Similarity NPC115466
0.5753 Remote Similarity NPC39657
0.5753 Remote Similarity NPC61604
0.5714 Remote Similarity NPC299144
0.5694 Remote Similarity NPC217635
0.5667 Remote Similarity NPC479028
0.5667 Remote Similarity NPC479031
0.5636 Remote Similarity NPC153149
0.5636 Remote Similarity NPC294470
0.5606 Remote Similarity NPC189115
0.5606 Remote Similarity NPC475096
0.56 Remote Similarity NPC46092
0.56 Remote Similarity NPC470950
0.56 Remote Similarity NPC163635
0.5574 Remote Similarity NPC210478
0.5571 Remote Similarity NPC79957
0.5571 Remote Similarity NPC279298
0.5556 Remote Similarity NPC276195
0.5556 Remote Similarity NPC212729
0.5556 Remote Similarity NPC604498
0.5526 Remote Similarity NPC486548
0.5526 Remote Similarity NPC129417
0.5526 Remote Similarity NPC283995
0.55 Remote Similarity NPC218685
0.55 Remote Similarity NPC49074
0.5479 Remote Similarity NPC93924
0.5455 Remote Similarity NPC217854
0.5455 Remote Similarity NPC269242
0.5441 Remote Similarity NPC148273
0.5439 Remote Similarity NPC609376
0.5429 Remote Similarity NPC286235
0.5424 Remote Similarity NPC48863
0.5424 Remote Similarity NPC251981
0.5424 Remote Similarity NPC13745
0.541 Remote Similarity NPC162093
0.5397 Remote Similarity NPC104167
0.5385 Remote Similarity NPC294166
0.5385 Remote Similarity NPC115022
0.5352 Remote Similarity NPC38041
0.5352 Remote Similarity NPC18979
0.5352 Remote Similarity NPC22150
0.5352 Remote Similarity NPC60249
0.5345 Remote Similarity NPC200092
0.5345 Remote Similarity NPC226712
0.5345 Remote Similarity NPC608788
0.5263 Remote Similarity NPC152722
0.5254 Remote Similarity NPC145900
0.52 Remote Similarity NPC43508
0.5195 Remote Similarity NPC185307
0.5167 Remote Similarity NPC610709
0.5161 Remote Similarity NPC205054
0.5161 Remote Similarity NPC479769
0.5161 Remote Similarity NPC23084
0.5161 Remote Similarity NPC604356
0.5152 Remote Similarity NPC134260
0.5139 Remote Similarity NPC476411
0.5135 Remote Similarity NPC76871
0.5128 Remote Similarity NPC486549
0.5128 Remote Similarity NPC470235
0.5088 Remote Similarity NPC192810
0.5085 Remote Similarity NPC12308
0.5082 Remote Similarity NPC310661
0.5079 Remote Similarity NPC481303
0.5077 Remote Similarity NPC232673
0.5077 Remote Similarity NPC247146
0.5077 Remote Similarity NPC97326
0.5075 Remote Similarity NPC479030
0.5063 Remote Similarity NPC486546

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC323467 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
0.5345 Remote Similarity NPD1091 Pre-clinical

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