Natural Product: NPC603856

Natural Product IDNPC603856
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CPPNFWGIJSYTAL-VREZJPALSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4866440
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 CPPNFWGIJSYTAL-VREZJPALSA-N
Standard InCHI InChI=1S/C30H26O16/c31-13-4-1-11(7-15(13)33)2-6-20(35)43-10-19-23(37)26(40)28(42)30(46-19)45-18-9-17-21(24(38)22(18)36)25(39)27(41)29(44-17)12-3-5-14(32)16(34)8-12/h1-9,19,23,26,28,30-34,36-38,40-42H,10H2/b6-2+/t19-,23-,26+,28-,30-/m1/s1
SMILES O=C(/C=C/c1ccc(O)c(O)c1)OC[C@H]1O[C@@H](Oc2cc3oc(-c4ccc(O)c(O)c4)c(O)c(=O)c3c(O)c2O)[C@H](O)[C@@H](O)[C@@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   642.12 Volume:   591.023
?
Van der Waals volume.
Dense:   1.086 LogP:   0.955
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.033
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.046
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The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   32.0
TPSA:   277.27
?
Topological Polar Surface Area.
H-Bond Acceptor:   16.0
H-Bond Donor:   10.0 Rings:   5.0
Heavy Atoms:   16.0

MedChem Properties

QED Drug-Likeness Score:   0.076 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.456 Fsp3:   0.2
MCE-18:   114.722
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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:   1 PAINS Alert:   1
Colloidal aggregators:   0.824 Fluc inhibitor:   0.719
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.937
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.813
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.2 Promiscuous compounds:   0.883

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.842 MDCK Permeability:   -4.792
Pgp-inhibitor:   0.0 Pgp-substrate:   0.002
PAMPA:   0.996
?
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):   0.746
20% Bioavailability (F20%):   0.998 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.043
Plasma Protein Binding (PPB):   84.636% Volume Distribution (VD):   -0.063
Fu: 11.796%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.781
BSEP inhibitor:   0.013

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:   0.02
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.78
?
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):  3.851 Half-life (T1/2):  4.21

ADMET: Toxicity

hERG Blockers:  0.031 hERG Blockers (10um):  0.597
Human Hepatotoxicity (H-HT):  0.349 Drug-induced Liver Injury (DILI):  0.977
AMES Toxicity:  0.768 Rat Oral Acute Toxicity:  0.082
Maximum Recommended Daily Dose:  0.397 Skin Sensitization:  1.0
Carcinogencity:  0.069 Eye Corrosion:  0.0
Eye Irritation:  0.768 Respiratory Toxicity:  0.013
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.899
Hematotoxicity:  0.011 Drug-induced Nephrotoxicity:  0.097
Genotoxicity:  0.952 RPMI-8226 Immunitoxicity:  0.027
A549 Cytotoxicity:  0.973 Hek293 Cytotoxicity:  0.325
BCF:   0.648
?
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:   3.619
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.863
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.539
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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
NPO27892 Eupatorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27892 Eupatorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27892 Eupatorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27892 Eupatorium glandulosum Species Asteraceae 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
NPT28438 Unchecked Unchecked n.a. IC50 = 790.0 nM PMID[33857371]

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 NPC603856 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
0.9213 High Similarity NPC599948
0.7065 Intermediate Similarity NPC477848
0.6869 Remote Similarity NPC80068
0.6832 Remote Similarity NPC81042
0.6635 Remote Similarity NPC480796
0.6593 Remote Similarity NPC245014
0.6505 Remote Similarity NPC214621
0.6505 Remote Similarity NPC34267
0.6296 Remote Similarity NPC139571
0.625 Remote Similarity NPC223426
0.5962 Remote Similarity NPC270675
0.5962 Remote Similarity NPC195685
0.5941 Remote Similarity NPC233994
0.5922 Remote Similarity NPC488364
0.5905 Remote Similarity NPC85751
0.5905 Remote Similarity NPC19240
0.5895 Remote Similarity NPC84265
0.5877 Remote Similarity NPC488078
0.5769 Remote Similarity NPC211532
0.5729 Remote Similarity NPC291296
0.5728 Remote Similarity NPC476871
0.5727 Remote Similarity NPC472993
0.5701 Remote Similarity NPC36138
0.5699 Remote Similarity NPC157898
0.5676 Remote Similarity NPC217520
0.5648 Remote Similarity NPC472994
0.5636 Remote Similarity NPC470416
0.5612 Remote Similarity NPC476864
0.5607 Remote Similarity NPC477629
0.56 Remote Similarity NPC476870
0.5586 Remote Similarity NPC477895
0.5534 Remote Similarity NPC67105
0.5421 Remote Similarity NPC476620
0.5347 Remote Similarity NPC476868
0.5339 Remote Similarity NPC488079
0.5327 Remote Similarity NPC470443
0.5253 Remote Similarity NPC58716
0.5204 Remote Similarity NPC238376
0.52 Remote Similarity NPC476867
0.5192 Remote Similarity NPC254540
0.5189 Remote Similarity NPC133984
0.5152 Remote Similarity NPC277205
0.5152 Remote Similarity NPC37919
0.5149 Remote Similarity NPC157816
0.5143 Remote Similarity NPC488081
0.5098 Remote Similarity NPC476866
0.5096 Remote Similarity NPC116864
0.5096 Remote Similarity NPC244776
0.5089 Remote Similarity NPC484301
0.505 Remote Similarity NPC117260
0.5049 Remote Similarity NPC488082

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC603856 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