Natural Product: NPC296651

Natural Product IDNPC296651
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WQZGKKKJIJFFOK-UZJJNQGWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 59083882
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

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 WQZGKKKJIJFFOK-UZJJNQGWSA-N
Standard InCHI InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2?,3-,4-,5?,6?/m0/s1
SMILES C(C1[C@@H]([C@@H](C(C(O)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   180.06 Volume:   156.517
?
Van der Waals volume.
Dense:   1.15 LogP:   -2.287
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -2.072
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.341
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   6.0
TPSA:   110.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   5.0 Rings:   1.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.29 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.595 Fsp3:   1.0
MCE-18:   22.667
?
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:   0.002 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.094
?
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:   0.464 Promiscuous compounds:   0.098

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.97 MDCK Permeability:   -4.752
Pgp-inhibitor:   0.0 Pgp-substrate:   0.798
PAMPA:   0.999
?
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):   0.103
20% Bioavailability (F20%):   0.087 30% Bioavailability (F30%):   0.215
50% Bioavailability (F50%):   0.843

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.195
Plasma Protein Binding (PPB):   31.533% Volume Distribution (VD):   -0.512
Fu: 75.54%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.399
OATP1B3 inhibitor:   0.781 BCRP inhibitor:   0.033
BSEP inhibitor:   0.013

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.007 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.913 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.803
HLM stability:   0.026
?
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):  1.67 Half-life (T1/2):  2.681

ADMET: Toxicity

hERG Blockers:  0.042 hERG Blockers (10um):  0.339
Human Hepatotoxicity (H-HT):  0.288 Drug-induced Liver Injury (DILI):  0.055
AMES Toxicity:  0.523 Rat Oral Acute Toxicity:  0.163
Maximum Recommended Daily Dose:  0.043 Skin Sensitization:  0.233
Carcinogencity:  0.174 Eye Corrosion:  0.008
Eye Irritation:  0.703 Respiratory Toxicity:  0.053
Drug-induced Neurotoxicity:  0.086 Ototoxicity:  0.851
Hematotoxicity:  0.124 Drug-induced Nephrotoxicity:  0.131
Genotoxicity:  0.017 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.013 Hek293 Cytotoxicity:  0.053
BCF:   0.085
?
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:   0.904
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   1.374
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   0.595
?
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
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2008.08.002]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(00)97029-8]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. root n.a. PMID[17396934]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota seeds n.a. n.a. PMID[18603435]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota Seeds n.a. n.a. PMID[20469887]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[26434122]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[9544568]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21707 Trichosanthes kirilowii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16194 Morus bombycis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4702 Trichosanthes rosthornii Species Cucurbitaceae 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 NPC296651 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 NPC73906
1.0 High Similarity NPC285364
1.0 High Similarity NPC255377
1.0 High Similarity NPC92246
1.0 High Similarity NPC165846
1.0 High Similarity NPC176017
1.0 High Similarity NPC21209
1.0 High Similarity NPC69445
1.0 High Similarity NPC289758
1.0 High Similarity NPC605355
0.6957 Remote Similarity NPC320189
0.5926 Remote Similarity NPC114208
0.5926 Remote Similarity NPC4884
0.5926 Remote Similarity NPC321087
0.5926 Remote Similarity NPC277475
0.5926 Remote Similarity NPC602568
0.5161 Remote Similarity NPC322801
0.5161 Remote Similarity NPC14144
0.5161 Remote Similarity NPC600826
0.5161 Remote Similarity NPC606475
0.5128 Remote Similarity NPC89145
0.5128 Remote Similarity NPC157514
0.5128 Remote Similarity NPC322314
0.5128 Remote Similarity NPC269166

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC296651 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
1.0 High Similarity NPD8997 Approved
1.0 High Similarity NPD8998 Phase 2
1.0 High Similarity NPD8999 Phase 4
1.0 High Similarity NPD9000 Phase 3
0.5161 Remote Similarity NPD9031 Approved
0.5161 Remote Similarity NPD9032 Phase 4
0.5161 Remote Similarity NPD9033 Approved

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