Natural Product: NPC257948

Natural Product IDNPC257948
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ANRLEQNQSYGXBB-DFWYDOINSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44539543
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

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 ANRLEQNQSYGXBB-DFWYDOINSA-N
Standard InCHI InChI=1S/C4H9NO3.ClH/c5-3(1-2-6)4(7)8;/h3,6H,1-2,5H2,(H,7,8);1H/t3-;/m0./s1
SMILES C(CO)[C@@H](C(=O)O)N.Cl

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   119.06 Volume:   112.471
?
Van der Waals volume.
Dense:   1.059 LogP:   -2.102
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.535
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.117
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   1.0
TPSA:   83.55
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   4.0 Rings:   0.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.435 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.656 Fsp3:   0.75
MCE-18:   2.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.129 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.01
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.83 Promiscuous compounds:   0.874

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.866 MDCK Permeability:   -4.952
Pgp-inhibitor:   0.0 Pgp-substrate:   0.409
PAMPA:   0.997
?
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):   0.0
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.002
50% Bioavailability (F50%):   0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.727 MRP1:   0.329
Plasma Protein Binding (PPB):   10.663% Volume Distribution (VD):   -0.299
Fu: 90.362%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.531
OATP1B3 inhibitor:   0.712 BCRP inhibitor:   0.001
BSEP inhibitor:   0.003

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.259 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.297 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.003
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.018
HLM stability:   0.0
?
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):  10.497 Half-life (T1/2):  1.677

ADMET: Toxicity

hERG Blockers:  0.029 hERG Blockers (10um):  0.13
Human Hepatotoxicity (H-HT):  0.311 Drug-induced Liver Injury (DILI):  0.007
AMES Toxicity:  0.686 Rat Oral Acute Toxicity:  0.209
Maximum Recommended Daily Dose:  0.011 Skin Sensitization:  0.97
Carcinogencity:  0.097 Eye Corrosion:  0.861
Eye Irritation:  0.97 Respiratory Toxicity:  0.113
Drug-induced Neurotoxicity:  0.251 Ototoxicity:  0.058
Hematotoxicity:  0.128 Drug-induced Nephrotoxicity:  0.778
Genotoxicity:  0.069 RPMI-8226 Immunitoxicity:  0.092
A549 Cytotoxicity:  0.001 Hek293 Cytotoxicity:  0.026
BCF:   0.215
?
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:   2.039
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.424
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.616
?
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
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15286289]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. fruit n.a. PMID[18020353]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20515057]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. seed n.a. PMID[20947202]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[22934600]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. whole plant n.a. PMID[23678820]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24253552]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Fruits n.a. n.a. PMID[30543429]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Fruits n.a. n.a. PMID[30848923]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[35108453]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[36903935]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37047195]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37179510]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38263385]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38380569]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39592457]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota Leaves n.a. n.a. PMID[8864235]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Wax n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15388 Eucalyptus globulus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22160 Polygonatum cyrtonema Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4545 Canavalia gladiata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7255 Pterocarpus indicus 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
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 NPC257948 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
0.95 High Similarity NPC49952
0.95 High Similarity NPC136476
0.6818 Remote Similarity NPC317691
0.6364 Remote Similarity NPC226265
0.6364 Remote Similarity NPC219143
0.6364 Remote Similarity NPC254482
0.6364 Remote Similarity NPC110533
0.5909 Remote Similarity NPC63621
0.5909 Remote Similarity NPC326992
0.5909 Remote Similarity NPC121517
0.5909 Remote Similarity NPC168375
0.5909 Remote Similarity NPC600066
0.56 Remote Similarity NPC153370
0.56 Remote Similarity NPC34908
0.5556 Remote Similarity NPC88898
0.5556 Remote Similarity NPC106216
0.5417 Remote Similarity NPC270805
0.5417 Remote Similarity NPC329263
0.5417 Remote Similarity NPC118459
0.5417 Remote Similarity NPC309658
0.5417 Remote Similarity NPC327698
0.5417 Remote Similarity NPC93888
0.5417 Remote Similarity NPC53449
0.5417 Remote Similarity NPC604272
0.5417 Remote Similarity NPC607953
0.5238 Remote Similarity NPC116709
0.5238 Remote Similarity NPC21290
0.5238 Remote Similarity NPC272614
0.52 Remote Similarity NPC245027
0.52 Remote Similarity NPC43169
0.52 Remote Similarity NPC162620
0.52 Remote Similarity NPC327895
0.52 Remote Similarity NPC62045
0.52 Remote Similarity NPC112224
0.52 Remote Similarity NPC601942
0.5172 Remote Similarity NPC611992

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC257948 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
0.6818 Remote Similarity NPD8214 Approved
0.6364 Remote Similarity NPD8215 Phase 4
0.6364 Remote Similarity NPD8216 Phase 3
0.6364 Remote Similarity NPD8217 Phase 3
0.56 Remote Similarity NPD8614 Pre-clinical
0.5417 Remote Similarity NPD8624 Phase 2
0.5417 Remote Similarity NPD8801 Phase 4
0.5238 Remote Similarity NPD8210 Phase 3
0.5238 Remote Similarity NPD8211 Approved
0.52 Remote Similarity NPD9018 Phase 3
0.5185 Remote Similarity NPD8871 Phase 4
0.5172 Remote Similarity NPD8208 Clinical (unspecified phase)
0.5172 Remote Similarity NPD8209 Phase 2
0.5161 Remote Similarity NPD9025 Phase 2

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