Natural Product: NPC600804

Natural Product IDNPC600804
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JCDDKPVUVBDMHS-ZSZRGSJWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4637368
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 JCDDKPVUVBDMHS-ZSZRGSJWSA-N
Standard InCHI InChI=1S/C18H21ClO6/c1-10-7-11(20)5-3-2-4-6-12(21)8-13-16(18(24)25-10)14(22)9-15(23)17(13)19/h3,5,9-11,20,22-23H,2,4,6-8H2,1H3/b5-3-/t10-,11+/m1/s1
SMILES C[C@@H]1C[C@@H](O)/C=CCCCC(=O)Cc2c(Cl)c(O)cc(O)c2C(=O)O1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   368.1 Volume:   354.905
?
Van der Waals volume.
Dense:   1.037 LogP:   2.025
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.187
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.975
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   21.0
TPSA:   104.06
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   3.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.48 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.24 Fsp3:   0.444
MCE-18:   53.077
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.382 Fluc inhibitor:   0.174
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.299
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.184
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.187 Promiscuous compounds:   0.239

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.239 MDCK Permeability:   -4.767
Pgp-inhibitor:   0.019 Pgp-substrate:   0.001
PAMPA:   0.182
?
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%):   0.002 30% Bioavailability (F30%):   0.024
50% Bioavailability (F50%):   0.369

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.023 MRP1:   0.947
Plasma Protein Binding (PPB):   93.149% Volume Distribution (VD):   -0.151
Fu: 4.687%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.157
OATP1B3 inhibitor:   0.963 BCRP inhibitor:   0.045
BSEP inhibitor:   0.978

ADMET: Metabolism

CYP1A2-inhibitor:   0.048 CYP1A2-substrate:   0.105
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.076
CYP2C9-inhibitor:   0.027 CYP2C9-substrate:   0.01
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.694
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   0.906
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.988
HLM stability:   0.845
?
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):  6.484 Half-life (T1/2):  1.38

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.168
Human Hepatotoxicity (H-HT):  0.503 Drug-induced Liver Injury (DILI):  0.596
AMES Toxicity:  0.812 Rat Oral Acute Toxicity:  0.376
Maximum Recommended Daily Dose:  0.936 Skin Sensitization:  1.0
Carcinogencity:  0.665 Eye Corrosion:  0.544
Eye Irritation:  0.971 Respiratory Toxicity:  0.521
Drug-induced Neurotoxicity:  0.502 Ototoxicity:  0.208
Hematotoxicity:  0.067 Drug-induced Nephrotoxicity:  0.952
Genotoxicity:  0.918 RPMI-8226 Immunitoxicity:  0.162
A549 Cytotoxicity:  0.715 Hek293 Cytotoxicity:  0.523
BCF:   0.48
?
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:   3.181
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.538
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.802
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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
NPO49886 Ilyonectria sp. sb65 Genus Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63047 Pochonia chlamydosporia TF-0480 Genus Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT2307 Cell line 769-P Homo sapiens Activity n.a. n.a. n.a. PMID[32323537]
NPT81 Cell line A549 Homo sapiens Activity n.a. n.a. n.a. PMID[32323537]
NPT393 Cell line HCT-116 Homo sapiens Activity n.a. n.a. n.a. PMID[32323537]
NPT27699 Cell line B-cell line Mus musculus IC50 = 21900.0 nM PMID[32323537]
NPT30089 Cell line T-cell n.a. IC50 > 25000.0 nM PMID[32323537]

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 NPC600804 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
0.7903 Intermediate Similarity NPC470081
0.6567 Remote Similarity NPC610827
0.6324 Remote Similarity NPC473696
0.6176 Remote Similarity NPC474096
0.6176 Remote Similarity NPC481130
0.6087 Remote Similarity NPC489258
0.6056 Remote Similarity NPC28669
0.5972 Remote Similarity NPC489257
0.5735 Remote Similarity NPC298401
0.5694 Remote Similarity NPC474061
0.5342 Remote Similarity NPC58653
0.5135 Remote Similarity NPC173352

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC600804 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