Natural Product: NPC489480

Natural Product IDNPC489480
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
WQVJHHACXVLGBL-VBCBMUHNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 117937126
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 WQVJHHACXVLGBL-VBCBMUHNSA-N
Standard InCHI InChI=1S/C56H98N16O13/c1-7-32(4)13-11-12-16-44(75)63-36(17-23-57)51(80)72-46(34(6)74)56(85)68-39(20-26-60)48(77)67-41-22-28-62-55(84)45(33(5)73)71-52(81)40(21-27-61)65-47(76)37(18-24-58)66-53(82)42(29-31(2)3)69-54(83)43(30-35-14-9-8-10-15-35)70-49(78)38(19-25-59)64-50(41)79/h8-10,14-15,31-34,36-43,45-46,73-74H,7,11-13,16-30,57-61H2,1-6H3,(H,62,84)(H,63,75)(H,64,79)(H,65,76)(H,66,82)(H,67,77)(H,68,85)(H,69,83)(H,70,78)(H,71,81)(H,72,80)/t32-,33+,34+,36-,37-,38+,39-,40-,41-,42-,43+,45-,46-/m0/s1
SMILES CC[C@H](C)CCCCC(=N[C@@H](CCN)C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CCN)C(=N[C@H]1CCN=C([C@H]([C@@H](C)O)N=C([C@H](CCN)N=C([C@H](CCN)N=C([C@H](CC(C)C)N=C([C@@H](Cc2ccccc2)N=C([C@@H](CCN)N=C1O)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1202.75 Volume:   1213.329
?
Van der Waals volume.
Dense:   0.991 LogP:   0.122
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.134
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.572
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   29.0 Rigid Bonds:   33.0
TPSA:   529.05
?
Topological Polar Surface Area.
H-Bond Acceptor:   29.0
H-Bond Donor:   23.0 Rings:   2.0
Heavy Atoms:   29.0

MedChem Properties

QED Drug-Likeness Score:   0.031 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.937 Fsp3:   0.696
MCE-18:   102.063
?
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:   0.336 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.011
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.599
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.008 Promiscuous compounds:   0.123

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.556 MDCK Permeability:   -5.542
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):   0.999
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:   0.078
Plasma Protein Binding (PPB):   48.04% Volume Distribution (VD):   -0.423
Fu: 43.855%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.594

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.875 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 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):  0.058 Half-life (T1/2):  2.802

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  1.0 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.087 Rat Oral Acute Toxicity:  0.058
Maximum Recommended Daily Dose:  0.053 Skin Sensitization:  1.0
Carcinogencity:  0.037 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.02
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.078 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.047
?
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:   2.999
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.715
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.548
?
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
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[26539973]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[27359053]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[28294609]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[28541699]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29019684]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29667822]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[32040324]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[32173199]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[32267694]
NPO40759 Okeania sp. Species Oscillatoriaceae Bacteria 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
NPT21762 Single protein Lysine-specific histone demethylase 1 Homo sapiens K = 157.0 nM PMID[36537915]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus Inhibition = 100.0 % PMID[32173199]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC n.a. n.a. n.a. PMID[36574364]
NPT23195 Subcellular Cell membrane Bacteria Activity n.a. n.a. n.a. PMID[36574364]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC n.a. n.a. n.a. PMID[36574364]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 6.2 ug.mL-1 PMID[36574364]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 1.5 ug.mL-1 PMID[36574364]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 0.7 ug.mL-1 PMID[36574364]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 580.0 nM PMID[36574364]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 0.7 ug.mL-1 PMID[36574364]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[38516601]
NPT19 Organism Escherichia coli Escherichia coli MIC = 0.7 ug.mL-1 PMID[36574364]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC n.a. n.a. n.a. PMID[36574364]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Activity n.a. n.a. n.a. PMID[38516601]
NPT19 Organism Escherichia coli Escherichia coli Inhibition = 100.0 % PMID[36574364]
NPT20950 Cell line Erythrocyte n.a. HC50 n.a. n.a. n.a. PMID[36574364]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC n.a. n.a. n.a. PMID[36574364]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 1.5 ug.mL-1 PMID[36574364]
NPT19 Organism Escherichia coli Escherichia coli MIC = 580.0 nM PMID[36574364]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC > 128.0 ug.mL-1 PMID[38516601]
NPT1531 Organism Enterococcus faecium Enterococcus faecium Activity n.a. n.a. n.a. PMID[38516601]
NPT314 Organism Bacillus cereus Bacillus cereus MIC n.a. n.a. n.a. PMID[36574364]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC = 0.7 ug.mL-1 PMID[36574364]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC n.a. n.a. n.a. PMID[36574364]

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 NPC489480 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 NPC487760
1.0 High Similarity NPC486161
0.9474 High Similarity NPC482042
0.9315 High Similarity NPC489368
0.7273 Intermediate Similarity NPC489369
0.7013 Intermediate Similarity NPC482041
0.6667 Remote Similarity NPC489370
0.5111 Remote Similarity NPC46427

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC489480 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