Natural Product: NPC489113

Natural Product IDNPC489113
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WUPXFGNCTYEWMM-RAKGIWIYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 21121150
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002319] Phenol esters

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 WUPXFGNCTYEWMM-RAKGIWIYSA-N
Standard InCHI InChI=1S/C23H32O3/c1-15-7-6-8-21-22(15,4)12-11-16(2)23(21,5)14-18-13-19(25)9-10-20(18)26-17(3)24/h7,9-10,13,16,21,25H,6,8,11-12,14H2,1-5H3/t16-,21+,22+,23+/m0/s1
SMILES CC1=CCC[C@@H]2[C@]1(C)CC[C@H](C)[C@@]2(C)Cc1cc(ccc1OC(=O)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   356.24 Volume:   393.883
?
Van der Waals volume.
Dense:   0.904 LogP:   4.137
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.649
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.037
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   18.0
TPSA:   46.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.432 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.974 Fsp3:   0.609
MCE-18:   75.514
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.435 Fluc inhibitor:   0.006
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.044
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.364 Promiscuous compounds:   0.11

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.663 MDCK Permeability:   -4.652
Pgp-inhibitor:   0.177 Pgp-substrate:   0.045
PAMPA:   0.159
?
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):   0.0
20% Bioavailability (F20%):   0.298 30% Bioavailability (F30%):   0.353
50% Bioavailability (F50%):   0.847

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.773 MRP1:   0.821
Plasma Protein Binding (PPB):   93.143% Volume Distribution (VD):   0.481
Fu: 6.456%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.988 BCRP inhibitor:   0.026
BSEP inhibitor:   0.995

ADMET: Metabolism

CYP1A2-inhibitor:   0.025 CYP1A2-substrate:   0.41
CYP2C19-inhibitor:   0.366 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.007 CYP2C9-substrate:   0.133
CYP2D6-inhibitor:   0.044 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   0.151 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.977
HLM stability:   0.998
?
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):  8.171 Half-life (T1/2):  0.398

ADMET: Toxicity

hERG Blockers:  0.039 hERG Blockers (10um):  0.374
Human Hepatotoxicity (H-HT):  0.479 Drug-induced Liver Injury (DILI):  0.351
AMES Toxicity:  0.287 Rat Oral Acute Toxicity:  0.418
Maximum Recommended Daily Dose:  0.402 Skin Sensitization:  0.966
Carcinogencity:  0.671 Eye Corrosion:  0.609
Eye Irritation:  0.916 Respiratory Toxicity:  0.656
Drug-induced Neurotoxicity:  0.338 Ototoxicity:  0.134
Hematotoxicity:  0.31 Drug-induced Nephrotoxicity:  0.125
Genotoxicity:  0.196 RPMI-8226 Immunitoxicity:  0.037
A549 Cytotoxicity:  0.572 Hek293 Cytotoxicity:  0.501
BCF:   1.998
?
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:   4.775
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.886
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.493
?
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
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[11374954]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[15921404]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[1593283]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[18198840]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. at 1020 m depth from Chuuk Atoll, Federated States of Micronesia n.a. PMID[18824352]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[20230038]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[26551342]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[26863083]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[27336796]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[32243140]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. Indo-Pacific n.a. PMID[7494145]
NPO32617 dysidea sp. Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[9748373]

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
NPT178 Individual protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 9500.0 nM PMID[27336796]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT913 Cell line CHO-K1 Cricetulus griseus IC50 > 27300.0 nM PMID[31253530]
NPT2 Others Unspecified n.a. IC50 = 13700.0 nM PMID[31253530]
NPT2 Others Unspecified n.a. IC50 > 27300.0 nM PMID[31253530]

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 NPC489113 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
0.7143 Intermediate Similarity NPC489114
0.6935 Remote Similarity NPC489115
0.6364 Remote Similarity NPC475896
0.6364 Remote Similarity NPC27956
0.6212 Remote Similarity NPC489117
0.6129 Remote Similarity NPC266937
0.6119 Remote Similarity NPC489112
0.5821 Remote Similarity NPC489116
0.5821 Remote Similarity NPC470770
0.5571 Remote Similarity NPC609727
0.5352 Remote Similarity NPC198616
0.5211 Remote Similarity NPC258856
0.5211 Remote Similarity NPC600514

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC489113 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