Natural Product: NPC472270

Natural Product IDNPC472270
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
XTKIFEUKAOFVDD-FJZFINPGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3357152
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 XTKIFEUKAOFVDD-FJZFINPGSA-N
Standard InCHI InChI=1S/C94H148O43/c1-15-89(10,118)25-17-19-40(3)76(115)131-72-56(101)41(4)126-84(75(72)132-77(116)43(33-95)20-18-26-90(11,119)16-2)125-39-51-61(106)63(108)74(136-81-68(113)64(109)70(42(5)127-81)133-80-69(114)71(49(99)37-122-80)134-78-65(110)57(102)46(96)34-120-78)85(129-51)137-86(117)94-30-29-87(6,7)31-45(94)44-21-22-53-91(12)27-24-55(88(8,9)52(91)23-28-92(53,13)93(44,14)32-54(94)100)130-82-67(112)62(107)60(105)50(128-82)38-124-83-73(59(104)48(98)36-123-83)135-79-66(111)58(103)47(97)35-121-79/h15-16,19-21,41-42,45-75,78-85,95-114,118-119H,1-2,17-18,22-39H2,3-14H3/b40-19+,43-20+/t41-,42-,45-,46+,47+,48-,49+,50+,51+,52-,53+,54+,55-,56-,57-,58-,59-,60+,61+,62-,63-,64-,65+,66+,67+,68+,69+,70-,71-,72+,73+,74+,75+,78-,79-,80-,81-,82-,83-,84+,85-,89-,90?,91-,92+,93+,94+/m0/s1
SMILES CC1C(C(C(C(O1)OCC2C(C(C(C(O2)OC(=O)C34CCC(CC3C5=CCC6C7(CCC(C(C7CCC6(C5(CC4O)C)C)(C)C)OC8C(C(C(C(O8)COC9C(C(C(CO9)O)O)OC1C(C(C(CO1)O)O)O)O)O)O)C)(C)C)OC1C(C(C(C(O1)C)OC1C(C(C(CO1)O)OC1C(C(C(CO1)O)O)O)O)O)O)O)O)OC(=O)C(=CCCC(C)(C=C)O)CO)OC(=O)C(=CCCC(C)(C=C)O)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1964.94 Volume:   1880.033
?
Van der Waals volume.
Dense:   1.045 LogP:   -0.364
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.542
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.387
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   34.0 Rigid Bonds:   81.0
TPSA:   662.41
?
Topological Polar Surface Area.
H-Bond Acceptor:   43.0
H-Bond Donor:   22.0 Rings:   13.0
Heavy Atoms:   43.0

MedChem Properties

QED Drug-Likeness Score:   0.01 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   8.524 Fsp3:   0.862
MCE-18:   295.429
?
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:   0.027 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.334
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.411 Promiscuous compounds:   0.002

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.328 MDCK Permeability:   -4.894
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
PAMPA:   1.0
?
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):   1.0
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   9.157% Volume Distribution (VD):   -0.476
Fu: 30.866%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.002
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.024 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.014 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
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):  -2.078 Half-life (T1/2):  6.252

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.183
Human Hepatotoxicity (H-HT):  0.119 Drug-induced Liver Injury (DILI):  0.062
AMES Toxicity:  0.683 Rat Oral Acute Toxicity:  0.014
Maximum Recommended Daily Dose:  0.203 Skin Sensitization:  0.019
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.183 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.013
Genotoxicity:  0.01 RPMI-8226 Immunitoxicity:  0.202
A549 Cytotoxicity:  0.005 Hek293 Cytotoxicity:  0.991
BCF:   -0.309
?
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:   4.219
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.941
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.409
?
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
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota anomalous fruits n.a. n.a. PMID[25442304]
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20608 Gleditsia sinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20608 Gleditsia sinensis 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
NPT380 Cell line U-251 Homo sapiens Activity = 29.22 % PMID[25442304]
NPT76 Cell line C6 Rattus norvegicus Activity = 26.53 % PMID[11975483]
NPT380 Cell line U-251 Homo sapiens IC50 = 43100.0 nM PMID[25442304]
NPT76 Cell line C6 Rattus norvegicus IC50 = 30260.0 nM PMID[15620238]

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 NPC472270 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 NPC112492
0.8067 Intermediate Similarity NPC23020
0.7945 Intermediate Similarity NPC472268
0.7895 Intermediate Similarity NPC472269
0.7801 Intermediate Similarity NPC102505
0.7801 Intermediate Similarity NPC488514
0.7755 Intermediate Similarity NPC297950
0.7394 Intermediate Similarity NPC309223
0.7357 Intermediate Similarity NPC13998
0.7095 Intermediate Similarity NPC8524
0.7047 Intermediate Similarity NPC33012
0.6972 Remote Similarity NPC85154
0.6824 Remote Similarity NPC224381
0.6644 Remote Similarity NPC70809
0.6415 Remote Similarity NPC484830
0.6374 Remote Similarity NPC488204
0.6338 Remote Similarity NPC104137
0.6338 Remote Similarity NPC26626
0.6243 Remote Similarity NPC488201
0.6242 Remote Similarity NPC473386
0.6235 Remote Similarity NPC322904
0.6216 Remote Similarity NPC471577
0.62 Remote Similarity NPC286457
0.6169 Remote Similarity NPC220160
0.6125 Remote Similarity NPC475177
0.6114 Remote Similarity NPC475527
0.6089 Remote Similarity NPC187497
0.6071 Remote Similarity NPC488526
0.6053 Remote Similarity NPC471580
0.6038 Remote Similarity NPC480421
0.6036 Remote Similarity NPC475444
0.6036 Remote Similarity NPC473679
0.6012 Remote Similarity NPC478559
0.6012 Remote Similarity NPC478560
0.5948 Remote Similarity NPC470876
0.5948 Remote Similarity NPC475514
0.5935 Remote Similarity NPC144644
0.5935 Remote Similarity NPC170407
0.592 Remote Similarity NPC324933
0.5917 Remote Similarity NPC485563
0.5886 Remote Similarity NPC68767
0.5879 Remote Similarity NPC329893
0.5866 Remote Similarity NPC174336
0.5866 Remote Similarity NPC488513
0.5833 Remote Similarity NPC37860
0.5824 Remote Similarity NPC311178
0.5813 Remote Similarity NPC480422
0.5795 Remote Similarity NPC319719
0.5786 Remote Similarity NPC293031
0.5781 Remote Similarity NPC475345
0.5779 Remote Similarity NPC473452
0.5733 Remote Similarity NPC123522
0.573 Remote Similarity NPC488200
0.5698 Remote Similarity NPC222951
0.5674 Remote Similarity NPC475599
0.5636 Remote Similarity NPC489208
0.5629 Remote Similarity NPC484831
0.5621 Remote Similarity NPC480423
0.5621 Remote Similarity NPC484829
0.5588 Remote Similarity NPC233223
0.5588 Remote Similarity NPC183816
0.5588 Remote Similarity NPC43589
0.5587 Remote Similarity NPC488203
0.5584 Remote Similarity NPC488560
0.557 Remote Similarity NPC236638
0.557 Remote Similarity NPC294453
0.5517 Remote Similarity NPC164389
0.5517 Remote Similarity NPC232237
0.5513 Remote Similarity NPC237191
0.547 Remote Similarity NPC488202
0.5465 Remote Similarity NPC300655
0.5465 Remote Similarity NPC196874
0.546 Remote Similarity NPC489209
0.546 Remote Similarity NPC153673
0.5439 Remote Similarity NPC329878
0.543 Remote Similarity NPC815
0.5414 Remote Similarity NPC265699
0.5389 Remote Similarity NPC475649
0.5376 Remote Similarity NPC475584
0.5376 Remote Similarity NPC475152
0.5375 Remote Similarity NPC481081
0.537 Remote Similarity NPC142151
0.5366 Remote Similarity NPC110385
0.5366 Remote Similarity NPC51099
0.5361 Remote Similarity NPC275225
0.535 Remote Similarity NPC4749
0.5349 Remote Similarity NPC475394
0.5346 Remote Similarity NPC41061
0.5346 Remote Similarity NPC227551
0.528 Remote Similarity NPC305981
0.5276 Remote Similarity NPC482010
0.5276 Remote Similarity NPC267694
0.527 Remote Similarity NPC105800
0.5256 Remote Similarity NPC123199
0.5253 Remote Similarity NPC481080
0.5251 Remote Similarity NPC113620
0.5247 Remote Similarity NPC261506
0.5247 Remote Similarity NPC4328
0.5244 Remote Similarity NPC250247
0.5223 Remote Similarity NPC475160
0.5223 Remote Similarity NPC473714
0.522 Remote Similarity NPC57484
0.5193 Remote Similarity NPC100612
0.5185 Remote Similarity NPC202828
0.5185 Remote Similarity NPC119592
0.516 Remote Similarity NPC476113
0.5153 Remote Similarity NPC302543
0.5132 Remote Similarity NPC481079
0.5128 Remote Similarity NPC79643
0.5127 Remote Similarity NPC283417
0.5127 Remote Similarity NPC200049
0.5125 Remote Similarity NPC476068
0.5125 Remote Similarity NPC21691
0.5105 Remote Similarity NPC1046
0.5086 Remote Similarity NPC45606
0.5068 Remote Similarity NPC173583
0.5065 Remote Similarity NPC207738
0.5064 Remote Similarity NPC60557
0.5064 Remote Similarity NPC67857

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC472270 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