Natural Product: NPC297768

Natural Product IDNPC297768
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Orizabin V
IUPAC Name n.a.
Synonyms Orizabin V
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL309074
PubChem CID 21635817
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

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 VTCACSFZWLHMDR-PIQVQLGRSA-N
Standard InCHI InChI=1S/C50H86O22/c1-9-11-17-20-30-21-18-15-13-12-14-16-19-22-32(53)67-43-40(70-47-38(59)37(58)39(28(7)63-47)68-46(61)25(4)26(5)52)29(8)64-50(44(43)69-45(60)24(3)10-2)72-42-36(57)34(55)31(23-51)66-49(42)71-41-35(56)33(54)27(6)62-48(41)65-30/h24-31,33-44,47-52,54-59H,9-23H2,1-8H3/t24-,25+,26+,27+,28+,29-,30-,31+,33+,34+,35-,36-,37+,38+,39+,40-,41+,42+,43+,44+,47-,48-,49-,50-/m0/s1
SMILES CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@H]([C@H](O[C@H]3[C@H](O[C@H]4[C@H](O1)O[C@H](C)[C@H]([C@@H]4O)O)O[C@H](CO)[C@H]([C@@H]3O)O)O[C@@H](C)[C@@H]2O[C@@H]1O[C@H](C)[C@H]([C@@H]([C@H]1O)O)OC(=O)[C@@H]([C@H](O)C)C)OC(=O)[C@H](CC)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1038.56 Volume:   1016.049
?
Van der Waals volume.
Dense:   1.022 LogP:   3.02
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.66
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.938
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   45.0
TPSA:   314.58
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   8.0 Rings:   5.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.074 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.596 Fsp3:   0.94
MCE-18:   109.979
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.972 Fluc inhibitor:   0.064
?
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:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.52 Promiscuous compounds:   0.295

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.79 MDCK Permeability:   -5.011
Pgp-inhibitor:   0.0 Pgp-substrate:   0.826
PAMPA:   0.984
?
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%):   0.006 30% Bioavailability (F30%):   0.993
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.539
Plasma Protein Binding (PPB):   70.517% Volume Distribution (VD):   -0.354
Fu: 20.554%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.011

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.013
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.995
HLM stability:   0.997
?
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):  0.846 Half-life (T1/2):  3.291

ADMET: Toxicity

hERG Blockers:  0.004 hERG Blockers (10um):  0.029
Human Hepatotoxicity (H-HT):  0.704 Drug-induced Liver Injury (DILI):  0.997
AMES Toxicity:  0.894 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.004 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.654 Drug-induced Nephrotoxicity:  0.98
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.582
A549 Cytotoxicity:  0.984 Hek293 Cytotoxicity:  0.181
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:   3.242
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.074
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.008
?
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
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota Roots Mexican n.a. PMID[10479311]
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota crude resin Mexican n.a. PMID[16562846]
NPO19009 Ipomoea orizabensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19009 Ipomoea orizabensis Species Convolvulaceae 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
NPT91 Cell line KB Homo sapiens ED50 = 7.0 ug ml-1 PMID[7381856]
NPT5198 Cell line OVCAR Homo sapiens ED50 > 15.0 ug ml-1 PMID[7381856]
NPT148 Cell line HCT-15 Homo sapiens ED50 > 15.0 ug ml-1 DOI[10.1007/s00044-010-9328-z]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 > 15.0 ug ml-1 PMID[10479311]

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 NPC297768 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
0.9459 High Similarity NPC478734
0.9211 High Similarity NPC478733
0.9079 High Similarity NPC477344
0.875 High Similarity NPC238264
0.875 High Similarity NPC477345
0.8415 Intermediate Similarity NPC478732
0.8313 Intermediate Similarity NPC475270
0.8313 Intermediate Similarity NPC475327
0.8293 Intermediate Similarity NPC476087
0.8293 Intermediate Similarity NPC475667
0.8161 Intermediate Similarity NPC475241
0.8095 Intermediate Similarity NPC224953
0.7975 Intermediate Similarity NPC22742
0.7975 Intermediate Similarity NPC477346
0.7882 Intermediate Similarity NPC184915
0.7882 Intermediate Similarity NPC126685
0.7738 Intermediate Similarity NPC478730
0.7701 Intermediate Similarity NPC44782
0.7674 Intermediate Similarity NPC183888
0.7614 Intermediate Similarity NPC475164
0.7529 Intermediate Similarity NPC119583
0.7528 Intermediate Similarity NPC473605
0.7528 Intermediate Similarity NPC475375
0.7471 Intermediate Similarity NPC259294
0.7356 Intermediate Similarity NPC238056
0.7356 Intermediate Similarity NPC478731
0.7356 Intermediate Similarity NPC115013
0.7326 Intermediate Similarity NPC143421
0.7308 Intermediate Similarity NPC606819
0.7241 Intermediate Similarity NPC483170
0.7209 Intermediate Similarity NPC477319
0.7159 Intermediate Similarity NPC290012
0.7126 Intermediate Similarity NPC307400
0.7126 Intermediate Similarity NPC472204
0.7126 Intermediate Similarity NPC27289
0.7111 Intermediate Similarity NPC476066
0.7045 Intermediate Similarity NPC478726
0.7011 Intermediate Similarity NPC173328
0.7 Intermediate Similarity NPC472200
0.7 Intermediate Similarity NPC475525
0.7 Intermediate Similarity NPC475540
0.6977 Remote Similarity NPC109887
0.6941 Remote Similarity NPC89843
0.6932 Remote Similarity NPC186992
0.6914 Remote Similarity NPC477350
0.69 Remote Similarity NPC600721
0.69 Remote Similarity NPC605872
0.6897 Remote Similarity NPC146992
0.6897 Remote Similarity NPC85759
0.686 Remote Similarity NPC477326
0.6818 Remote Similarity NPC472205
0.6813 Remote Similarity NPC123204
0.6742 Remote Similarity NPC294748
0.6739 Remote Similarity NPC477347
0.6706 Remote Similarity NPC477349
0.67 Remote Similarity NPC610996
0.6667 Remote Similarity NPC479059
0.6667 Remote Similarity NPC600446
0.6667 Remote Similarity NPC605013
0.6552 Remote Similarity NPC477331
0.6552 Remote Similarity NPC477332
0.6517 Remote Similarity NPC478722
0.6517 Remote Similarity NPC267592
0.6517 Remote Similarity NPC478725
0.6489 Remote Similarity NPC478728
0.6444 Remote Similarity NPC478723
0.6444 Remote Similarity NPC478724
0.6421 Remote Similarity NPC478727
0.6413 Remote Similarity NPC169345
0.6413 Remote Similarity NPC477317
0.6413 Remote Similarity NPC477318
0.6333 Remote Similarity NPC479061
0.6333 Remote Similarity NPC60849
0.6322 Remote Similarity NPC113745
0.6322 Remote Similarity NPC477320
0.6322 Remote Similarity NPC477323
0.6322 Remote Similarity NPC477325
0.6322 Remote Similarity NPC609436
0.6286 Remote Similarity NPC600940
0.6279 Remote Similarity NPC281563
0.6275 Remote Similarity NPC611287
0.6264 Remote Similarity NPC479058
0.6264 Remote Similarity NPC479060
0.625 Remote Similarity NPC604005
0.625 Remote Similarity NPC605014
0.6132 Remote Similarity NPC610997
0.6117 Remote Similarity NPC290276
0.6111 Remote Similarity NPC158302
0.602 Remote Similarity NPC477348
0.5926 Remote Similarity NPC472352
0.5905 Remote Similarity NPC600672
0.5882 Remote Similarity NPC478729
0.5876 Remote Similarity NPC269318
0.5862 Remote Similarity NPC146380
0.5789 Remote Similarity NPC206823
0.5739 Remote Similarity NPC147032
0.5618 Remote Similarity NPC477328
0.5618 Remote Similarity NPC477330
0.5577 Remote Similarity NPC63404
0.5556 Remote Similarity NPC477329
0.5536 Remote Similarity NPC471024
0.5524 Remote Similarity NPC77651
0.5514 Remote Similarity NPC10121
0.5514 Remote Similarity NPC198918
0.5514 Remote Similarity NPC10883
0.551 Remote Similarity NPC479057
0.5429 Remote Similarity NPC35338
0.5429 Remote Similarity NPC204214
0.5429 Remote Similarity NPC92283
0.5377 Remote Similarity NPC28069
0.53 Remote Similarity NPC163409
0.5165 Remote Similarity NPC475425
0.5135 Remote Similarity NPC471025
0.5088 Remote Similarity NPC471026
0.5047 Remote Similarity NPC124878
0.5047 Remote Similarity NPC231888

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC297768 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
NPD

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