Natural Product: NPC98163

Natural Product IDNPC98163
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KZSNJWFQEVHDMF-XFILSWFESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11829420
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:0004310] Valine and derivatives

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 KZSNJWFQEVHDMF-XFILSWFESA-N
Standard InCHI InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1/i1D3,6+1/t3?,4-
SMILES C(C(C)[C@@H](C(=O)O)[15NH2])([2H])([2H])[2H]

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   121.09 Volume:   120.977
?
Van der Waals volume.
Dense:   1.001 LogP:   -1.257
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.015
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.803
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   1.0
TPSA:   63.32
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.519 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.411 Fsp3:   0.8
MCE-18:   6.0
?
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:   0.34 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
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:   0.751 Promiscuous compounds:   0.633

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.529 MDCK Permeability:   -5.184
Pgp-inhibitor:   0.0 Pgp-substrate:   0.004
PAMPA:   0.857
?
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%):   0.0
50% Bioavailability (F50%):   0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.028 MRP1:   0.934
Plasma Protein Binding (PPB):   37.558% Volume Distribution (VD):   0.102
Fu: 60.617%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.749
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.0
BSEP inhibitor:   0.54

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.003 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.013 CYP2C9-substrate:   0.009
CYP2D6-inhibitor:   0.292 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.003
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.043
HLM stability:   0.005
?
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):  3.122 Half-life (T1/2):  1.584

ADMET: Toxicity

hERG Blockers:  0.072 hERG Blockers (10um):  0.301
Human Hepatotoxicity (H-HT):  0.944 Drug-induced Liver Injury (DILI):  0.979
AMES Toxicity:  0.058 Rat Oral Acute Toxicity:  0.55
Maximum Recommended Daily Dose:  0.985 Skin Sensitization:  0.999
Carcinogencity:  0.042 Eye Corrosion:  0.226
Eye Irritation:  0.909 Respiratory Toxicity:  0.269
Drug-induced Neurotoxicity:  0.01 Ototoxicity:  0.99
Hematotoxicity:  0.047 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.001
A549 Cytotoxicity:  0.007 Hek293 Cytotoxicity:  0.067
BCF:   0.192
?
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:   2.844
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.086
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.305
?
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
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. DOI[10.2478/s11535-012-0017-4]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. seed n.a. PMID[10898633]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. PMID[30892891]
NPO5939 Semen sojae praeparata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16309 Semen astragali complanati n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO15173 Concha meretricis seu cyclinae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12126.1 Coix lacryma- jobi var. ma - yuen Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16309 Semen astragali complanati n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15173 Concha meretricis seu cyclinae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12126.1 Coix lacryma- jobi var. ma - yuen Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5939 Semen sojae praeparata n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29390 Semen juglandis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1150 Juncus effusus Species Juncaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20898 Agaricus bisporus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26343 Fagopyrum esculentum Species Polygonaceae 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 NPC98163 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
0.7368 Intermediate Similarity NPC132307
0.7368 Intermediate Similarity NPC126925
0.6667 Remote Similarity NPC116709
0.6667 Remote Similarity NPC21290
0.6667 Remote Similarity NPC272614
0.6364 Remote Similarity NPC84636
0.6364 Remote Similarity NPC226027
0.6364 Remote Similarity NPC174246
0.6364 Remote Similarity NPC43204
0.5833 Remote Similarity NPC190385
0.5714 Remote Similarity NPC63621
0.5714 Remote Similarity NPC326992
0.5714 Remote Similarity NPC121517
0.5714 Remote Similarity NPC168375
0.5714 Remote Similarity NPC600066
0.5652 Remote Similarity NPC245027
0.5652 Remote Similarity NPC162620
0.5652 Remote Similarity NPC62045
0.5238 Remote Similarity NPC237525
0.5238 Remote Similarity NPC326212
0.5217 Remote Similarity NPC270805
0.5217 Remote Similarity NPC118459
0.5217 Remote Similarity NPC327698
0.5217 Remote Similarity NPC93888
0.5217 Remote Similarity NPC53449

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC98163 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
0.7368 Intermediate Similarity NPD8798 Phase 2
0.6667 Remote Similarity NPD8210 Phase 3
0.6667 Remote Similarity NPD8211 Approved
0.6364 Remote Similarity NPD9017 Phase 2
0.5833 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5652 Remote Similarity NPD9018 Phase 3
0.5217 Remote Similarity NPD8624 Phase 2
0.5217 Remote Similarity NPD8801 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