Natural Product: NPC604059

Natural Product IDNPC604059
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
BFWVEYLLAWYDQP-WSNTWWIMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3115747
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0003297] Organic Polymers
      • [CHEMONTID:0003298] Polypeptides

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 BFWVEYLLAWYDQP-WSNTWWIMSA-N
Standard InCHI InChI=1S/C73H115N17O20/c1-10-40(7)21-22-45(93)33-56(94)88-59(38(3)4)70(106)84-49(25-28-74)62(98)78-35-57(95)80-54(36-91)68(104)86-53(32-44-34-77-47-20-16-15-19-46(44)47)67(103)87-55(37-92)69(105)83-50(26-29-75)63(99)82-51(27-30-76)64(100)85-52(31-43-17-13-12-14-18-43)66(102)81-48(23-24-58(96)97)65(101)89-60(39(5)6)71(107)90-61(41(8)11-2)72(108)79-42(9)73(109)110/h12-20,34,38-42,45,48-55,59-61,77,91-93H,10-11,21-33,35-37,74-76H2,1-9H3,(H,78,98)(H,79,108)(H,80,95)(H,81,102)(H,82,99)(H,83,105)(H,84,106)(H,85,100)(H,86,104)(H,87,103)(H,88,94)(H,89,101)(H,90,107)(H,96,97)(H,109,110)/t40-,41-,42-,45+,48-,49+,50-,51+,52-,53+,54+,55-,59+,60-,61+/m0/s1
SMILES CC[C@H](C)CC[C@@H](O)CC(=O)N[C@@H](C(=O)N[C@H](CCN)C(=O)NCC(=O)N[C@H](CO)C(=O)N[C@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](CO)C(=O)N[C@@H](CCN)C(=O)N[C@H](CCN)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@@H](C)C(=O)O)[C@@H](C)CC)C(C)C)C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1549.85 Volume:   1550.241
?
Van der Waals volume.
Dense:   1.0 LogP:   0.587
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.353
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.022
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The logarithm of aqueous solubility value.
Rotatable Bonds:   64.0 Rigid Bonds:   31.0
TPSA:   607.44
?
Topological Polar Surface Area.
H-Bond Acceptor:   37.0
H-Bond Donor:   25.0 Rings:   3.0
Heavy Atoms:   37.0

MedChem Properties

QED Drug-Likeness Score:   0.025 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.881 Fsp3:   0.603
MCE-18:   90.0
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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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.638 Fluc inhibitor:   0.014
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.113
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.662
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.011 Promiscuous compounds:   0.292

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.713 MDCK Permeability:   -5.095
Pgp-inhibitor:   0.992 Pgp-substrate:   0.0
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):   1.0
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:   0.0
Plasma Protein Binding (PPB):   31.299% Volume Distribution (VD):   -0.483
Fu: 65.947%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   1.0

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:   0.0
CYP3A4-inhibitor:   0.0 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):  1.089 Half-life (T1/2):  1.347

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.003 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.03 Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.641 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.957 Ototoxicity:  1.0
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.001
BCF:   0.22
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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:   3.309
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.289
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.264
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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
NPO43312 Paenibacillus terrae NRRL B-30644 Genus Paenibacillaceae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT71 Cell line HEK293 Homo sapiens MIC = 200.0 ug.mL-1 PMID[24479847]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC = 6.25 ug.mL-1 PMID[24479847]
NPT2910 Organism Campylobacter jejuni Campylobacter jejuni MIC = 1.56 ug.mL-1 PMID[24479847]
NPT564 Organism Listeria monocytogenes Listeria monocytogenes MIC = 50.0 ug.mL-1 PMID[24479847]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 3.13 ug.mL-1 PMID[24479847]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 50.0 ug.mL-1 PMID[24479847]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 100.0 ug.mL-1 PMID[24479847]
NPT19 Organism Escherichia coli Escherichia coli MIC = 3.13 ug.mL-1 PMID[24479847]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100.0 ug.mL-1 PMID[24479847]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC = 12.5 ug.mL-1 PMID[24479847]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC > 100.0 ug.mL-1 PMID[24479847]

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 NPC604059 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
0.5862 Remote Similarity NPC604088
0.5714 Remote Similarity NPC601264
0.5705 Remote Similarity NPC607485
0.5696 Remote Similarity NPC610952
0.5603 Remote Similarity NPC610128
0.5449 Remote Similarity NPC600998
0.5449 Remote Similarity NPC611186
0.5385 Remote Similarity NPC477630
0.5337 Remote Similarity NPC609988
0.5306 Remote Similarity NPC323927
0.5294 Remote Similarity NPC600192
0.5294 Remote Similarity NPC605408
0.521 Remote Similarity NPC601302
0.52 Remote Similarity NPC601205
0.5122 Remote Similarity NPC611717
0.5039 Remote Similarity NPC603279
0.5032 Remote Similarity NPC601051
0.5032 Remote Similarity NPC609990
0.503 Remote Similarity NPC607277

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC604059 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