Natural Product: NPC488618

Natural Product IDNPC488618
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ITCLZCQAYVLWPY-LDTNTTFZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44584017
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 ITCLZCQAYVLWPY-LDTNTTFZSA-N
Standard InCHI InChI=1S/C73H112N2O32/c1-28-45(81)51(87)58(105-63-55(91)47(83)36(79)26-96-63)65(98-28)97-27-38-49(85)50(86)44(75-30(3)77)61(101-38)103-42-18-19-70(8)39(69(42,6)7)17-20-71(9)40(70)16-15-32-33-21-68(4,5)43(102-60(93)31-13-11-12-14-34(31)74)23-73(33,41(80)22-72(32,71)10)67(94)107-66-59(52(88)48(84)37(24-76)100-66)106-64-56(92)53(89)57(29(2)99-64)104-62-54(90)46(82)35(78)25-95-62/h11-15,28-29,33,35-59,61-66,76,78-92H,16-27,74H2,1-10H3,(H,75,77)/t28-,29+,33+,35-,36-,37-,38-,39+,40-,41-,42+,43+,44-,45+,46+,47+,48-,49-,50-,51+,52+,53+,54-,55-,56-,57+,58-,59-,61+,62+,63+,64+,65-,66+,70+,71-,72-,73-/m1/s1
SMILES C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)O[C@H]2CC[C@@]3(C)[C@@H](CC[C@]4(C)[C@@H]3CC=C3[C@@H]5CC(C)(C)[C@H](C[C@@]5([C@@H](C[C@@]43C)O)C(=O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O)OC(=O)c3ccccc3N)C2(C)C)N=C(C)O)O)O)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1528.72 Volume:   1453.311
?
Van der Waals volume.
Dense:   1.052 LogP:   0.054
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.905
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.292
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   19.0 Rigid Bonds:   71.0
TPSA:   536.42
?
Topological Polar Surface Area.
H-Bond Acceptor:   34.0
H-Bond Donor:   19.0 Rings:   12.0
Heavy Atoms:   34.0

MedChem Properties

QED Drug-Likeness Score:   0.019 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.646 Fsp3:   0.849
MCE-18:   351.63
?
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:   0.864 Fluc inhibitor:   0.03
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.159
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.076 Promiscuous compounds:   0.049

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.687 MDCK Permeability:   -5.039
Pgp-inhibitor:   0.0 Pgp-substrate:   0.915
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):   0.141
20% Bioavailability (F20%):   0.063 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.001
Plasma Protein Binding (PPB):   64.824% Volume Distribution (VD):   -0.391
Fu: 26.639%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

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:   0.0
CYP3A4-inhibitor:   0.096 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.006
?
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):  -1.032 Half-life (T1/2):  5.013

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.956 Drug-induced Liver Injury (DILI):  0.999
AMES Toxicity:  0.994 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.004 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.598 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.986 RPMI-8226 Immunitoxicity:  0.278
A549 Cytotoxicity:  0.594 Hek293 Cytotoxicity:  0.527
BCF:   0.502
?
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:   3.764
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.999
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.731
?
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
NPO7820 Albizia grandibracteata Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[15974615]
NPO7820 Albizia grandibracteata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7820 Albizia grandibracteata 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
NPT91 Cell line KB Homo sapiens IC50 = 1300.0 nM PMID[15974615]
NPT83 Cell line MCF7 Homo sapiens IC50 = 400.0 nM PMID[15974615]

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 NPC488618 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
0.9632 High Similarity NPC488619
0.9155 High Similarity NPC488620
0.7351 Intermediate Similarity NPC13989
0.7134 Intermediate Similarity NPC113620
0.7037 Intermediate Similarity NPC172365
0.6975 Remote Similarity NPC265699
0.6937 Remote Similarity NPC100612
0.6867 Remote Similarity NPC174336
0.6706 Remote Similarity NPC187497
0.6522 Remote Similarity NPC207738
0.6475 Remote Similarity NPC210729
0.6475 Remote Similarity NPC82931
0.6442 Remote Similarity NPC482013
0.6433 Remote Similarity NPC329893
0.6319 Remote Similarity NPC222951
0.6273 Remote Similarity NPC300655
0.6273 Remote Similarity NPC196874
0.6258 Remote Similarity NPC478559
0.6258 Remote Similarity NPC478560
0.6164 Remote Similarity NPC484830
0.6062 Remote Similarity NPC484831
0.6061 Remote Similarity NPC311178
0.6049 Remote Similarity NPC484829
0.6023 Remote Similarity NPC319719
0.6012 Remote Similarity NPC233223
0.6012 Remote Similarity NPC183816
0.6012 Remote Similarity NPC43589
0.5975 Remote Similarity NPC475177
0.5971 Remote Similarity NPC105800
0.5906 Remote Similarity NPC322904
0.5894 Remote Similarity NPC470876
0.5854 Remote Similarity NPC329878
0.5799 Remote Similarity NPC475444
0.5799 Remote Similarity NPC473679
0.578 Remote Similarity NPC324933
0.5776 Remote Similarity NPC489208
0.5705 Remote Similarity NPC482010
0.5696 Remote Similarity NPC489209
0.565 Remote Similarity NPC488201
0.5616 Remote Similarity NPC104137
0.5616 Remote Similarity NPC26626
0.5577 Remote Similarity NPC309223
0.5536 Remote Similarity NPC220838
0.5535 Remote Similarity NPC102505
0.5535 Remote Similarity NPC488514
0.5533 Remote Similarity NPC243680
0.5497 Remote Similarity NPC603137
0.5467 Remote Similarity NPC123522
0.5455 Remote Similarity NPC232237
0.5419 Remote Similarity NPC488204
0.5419 Remote Similarity NPC286457
0.5333 Remote Similarity NPC488202
0.5294 Remote Similarity NPC45606
0.529 Remote Similarity NPC85154
0.5276 Remote Similarity NPC120667
0.5276 Remote Similarity NPC278272
0.5276 Remote Similarity NPC8524
0.5244 Remote Similarity NPC33012
0.5232 Remote Similarity NPC185466
0.5155 Remote Similarity NPC70809
0.5127 Remote Similarity NPC13998
0.5123 Remote Similarity NPC482011
0.511 Remote Similarity NPC488203
0.5108 Remote Similarity NPC476113
0.5098 Remote Similarity NPC473824
0.5098 Remote Similarity NPC610204
0.5067 Remote Similarity NPC481079
0.5031 Remote Similarity NPC473452
0.5031 Remote Similarity NPC220160

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488618 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