Natural Product: NPC480541

Natural Product IDNPC480541
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ICQSKMCOEYNHHW-CSCRWWNNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000348] Peptides
            • [CHEMONTID:0004831] Oligopeptides

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 ICQSKMCOEYNHHW-CSCRWWNNSA-N
Standard InCHI InChI=1S/C53H95N7O14/c1-14-34(12)26-35(13)18-16-15-17-19-36(61)27-43(62)54-37(20-21-44(63)64)47(67)55-38(22-29(2)3)48(68)57-40(24-31(6)7)51(71)60-46(33(10)11)52(72)58-41(28-45(65)66)50(70)56-39(23-30(4)5)49(69)59-42(53(73)74)25-32(8)9/h29-42,46,61H,14-28H2,1-13H3,(H,54,62)(H,55,67)(H,56,70)(H,57,68)(H,58,72)(H,59,69)(H,60,71)(H,63,64)(H,65,66)(H,73,74)/t34?,35?,36-,37+,38+,39+,40+,41+,42+,46-/m1/s1
SMILES CCC(C)CC(C)CCCCC[C@H](CC(=N[C@@H](CCC(=O)O)C(=N[C@@H](CC(C)C)C(=N[C@@H](CC(C)C)C(=N[C@H](C(C)C)C(=N[C@@H](CC(=O)O)C(=N[C@@H](CC(C)C)C(=N[C@@H](CC(C)C)C(=O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1053.69 Volume:   1098.92
?
Van der Waals volume.
Dense:   0.959 LogP:   7.645
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.271
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.492
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   39.0 Rigid Bonds:   10.0
TPSA:   360.26
?
Topological Polar Surface Area.
H-Bond Acceptor:   21.0
H-Bond Donor:   11.0 Rings:   0.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.015 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.391 Fsp3:   0.811
MCE-18:   25.0
?
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:   0.528 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.353
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.063 Promiscuous compounds:   0.098

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.424 MDCK Permeability:   -5.019
Pgp-inhibitor:   0.0 Pgp-substrate:   0.006
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):   0.993
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:   0.256
Plasma Protein Binding (PPB):   80.785% Volume Distribution (VD):   -0.208
Fu: 20.136%
?
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:   1.0 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 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):  0.181 Half-life (T1/2):  3.21

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:  0.019 Rat Oral Acute Toxicity:  0.156
Maximum Recommended Daily Dose:  0.707 Skin Sensitization:  1.0
Carcinogencity:  0.001 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.761
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.872
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.277
?
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:   3.51
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.382
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.457
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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
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[11112781]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[153409]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[21673922]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23265519]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23317005]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23488669]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[27524650]
NPO40751 Marine Bacteria (Unclassified) n.a. n.a. n.a. n.a. n.a. n.a. PMID[28362500]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[29115831]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[31287310]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO40751 Marine Bacteria (Unclassified) n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria 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
NPT529 Organism Rhizoctonia solani Rhizoctonia solani MIC = 4.0 ug.mL-1 PMID[31287310]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 32.0 ug.mL-1 PMID[28362500]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana MIC = 4.0 ug.mL-1 PMID[31287310]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 16.0 ug.mL-1 PMID[28362500]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 16.0 ug.mL-1 PMID[28362500]
NPT1096 Organism Colletotrichum acutatum Colletotrichum acutatum MIC = 4.0 ug.mL-1 PMID[31287310]
NPT1242 Organism Salmonella typhi Salmonella enterica subsp. enterica serovar Typhi MIC = 32.0 ug.mL-1 PMID[28362500]

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 NPC480541 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
0.9324 High Similarity NPC480540
0.8356 Intermediate Similarity NPC487004
0.7162 Intermediate Similarity NPC487002
0.6118 Remote Similarity NPC487003
0.549 Remote Similarity NPC481739
0.549 Remote Similarity NPC481741
0.5446 Remote Similarity NPC481737
0.5217 Remote Similarity NPC227051
0.5204 Remote Similarity NPC487154
0.5204 Remote Similarity NPC279592
0.5204 Remote Similarity NPC489614
0.5204 Remote Similarity NPC485875
0.5196 Remote Similarity NPC481740

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480541 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