Natural Product: NPC486514

Natural Product IDNPC486514
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
LNKLNUAMTRHBLB-IPGAQVEVSA-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]

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 LNKLNUAMTRHBLB-IPGAQVEVSA-N
Standard InCHI InChI=1S/C133H207N37O39S6/c1-14-65(9)102-127(204)143-50-97(179)146-88-58-211-210-57-87-108(185)142-49-96(178)145-78(38-39-99(181)182)111(188)154-84(54-173)118(195)159-91-61-214-212-59-89(158-119(196)85(55-174)156-120(88)197)121(198)149-75(29-20-22-40-134)110(187)153-83(53-172)116(193)148-76(30-21-23-41-135)112(189)164-101(64(7)8)129(206)162-90(122(199)150-79(45-70-34-36-72(176)37-35-70)113(190)147-77(31-24-42-139-133(137)138)109(186)151-81(47-95(136)177)107(184)141-51-98(180)163-104(67(11)16-3)131(208)169-43-25-32-93(169)125(202)160-87)60-213-215-62-92(124(201)167-103(66(10)15-2)130(207)157-86(56-175)117(194)155-82(52-171)115(192)144-69(13)106(183)166-102)161-126(203)94-33-26-44-170(94)132(209)105(68(12)17-4)168-114(191)80(152-128(205)100(63(5)6)165-123(91)200)46-71-48-140-74-28-19-18-27-73(71)74/h18-19,27-28,34-37,48,63-69,75-94,100-105,140,171-176H,14-17,20-26,29-33,38-47,49-62,134-135H2,1-13H3,(H2,136,177)(H,141,184)(H,142,185)(H,143,204)(H,144,192)(H,145,178)(H,146,179)(H,147,190)(H,148,193)(H,149,198)(H,150,199)(H,151,186)(H,152,205)(H,153,187)(H,154,188)(H,155,194)(H,156,197)(H,157,207)(H,158,196)(H,159,195)(H,160,202)(H,161,203)(H,162,206)(H,163,180)(H,164,189)(H,165,200)(H,166,183)(H,167,201)(H,168,191)(H,181,182)(H4,137,138,139)/t65-,66-,67-,68-,69-,75-,76-,77+,78-,79-,80-,81-,82-,83+,84-,85-,86-,87-,88-,89?,90-,91-,92-,93-,94-,100-,101-,102-,103-,104-,105-/m0/s1
SMILES CC[C@H](C)[C@H]1C(=NCC(=N[C@H]2CSSC[C@H]3C(=NCC(=N[C@@H](CCC(=O)O)C(=N[C@@H](CO)C(=N[C@H]4CSSCC(C(=N[C@@H](CCCCN)C(=N[C@H](CO)C(=N[C@@H](CCCCN)C(=N[C@@H](C(C)C)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H]([C@@H](C)CC)C(=N[C@@H](CO)C(=N[C@@H](CO)C(=N[C@@H](C)C(=N1)O)O)O)O)O)N=C([C@@H]1CCCN1C(=O)[C@H]([C@@H](C)CC)N=C([C@H](Cc1c[nH]c5ccccc15)N=C([C@H](C(C)C)N=C4O)O)O)O)C(=N[C@@H](Cc1ccc(cc1)O)C(=N[C@H](CCCNC(=N)N)C(=N[C@@H](CC(=N)O)C(=NCC(=N[C@@H]([C@@H](C)CC)C(=O)N1CCC[C@H]1C(=N3)O)O)O)O)O)O)O)O)O)O)O)N=C([C@H](CO)N=C2O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   3138.37 Volume:   2987.209
?
Van der Waals volume.
Dense:   1.051 LogP:   -7.78
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -2.964
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.905
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The logarithm of aqueous solubility value.
Rotatable Bonds:   37.0 Rigid Bonds:   134.0
TPSA:   1285.63
?
Topological Polar Surface Area.
H-Bond Acceptor:   76.0
H-Bond Donor:   46.0 Rings:   10.0
Heavy Atoms:   82.0

MedChem Properties

QED Drug-Likeness Score:   0.008 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.926 Fsp3:   0.647
MCE-18:   338.356
?
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:   0.333 Fluc inhibitor:   0.288
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.341
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.347
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.792 Promiscuous compounds:   0.164

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.257 MDCK Permeability:   -5.561
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):   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:   0.44
Plasma Protein Binding (PPB):   -6.342% Volume Distribution (VD):   -0.722
Fu: 163.999%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.031

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.996 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.007 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 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):  -4.184 Half-life (T1/2):  10.58

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:  0.0 Rat Oral Acute Toxicity:  0.944
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.97 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.035
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  1.0 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.4
?
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:   3.193
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.734
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.149
?
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
NPO40393 Viola inconspicua Species Violaceae Eukaryota n.a. n.a. n.a. PMID[31464123]
NPO40393 Viola inconspicua Species Violaceae 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
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC < 12500.0 nM PMID[31464123]
NPT19 Organism Escherichia coli Escherichia coli MIC = 5000.0 nM PMID[31464123]

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 NPC486514 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 NPC486506
1.0 High Similarity NPC485247
0.9869 High Similarity NPC477635
0.9264 High Similarity NPC329843
0.8988 High Similarity NPC486517
0.8263 Intermediate Similarity NPC484965
0.8025 Intermediate Similarity NPC477632
0.8025 Intermediate Similarity NPC486505
0.7988 Intermediate Similarity NPC486515
0.7636 Intermediate Similarity NPC486507
0.7636 Intermediate Similarity NPC485115
0.7528 Intermediate Similarity NPC477633
0.7456 Intermediate Similarity NPC484365
0.7412 Intermediate Similarity NPC484964
0.7391 Intermediate Similarity NPC489512
0.7293 Intermediate Similarity NPC477634
0.7278 Intermediate Similarity NPC485244
0.7273 Intermediate Similarity NPC479082
0.7222 Intermediate Similarity NPC485114
0.7166 Intermediate Similarity NPC479083
0.6977 Remote Similarity NPC485246
0.6949 Remote Similarity NPC486503
0.6919 Remote Similarity NPC484963
0.6914 Remote Similarity NPC485243
0.6893 Remote Similarity NPC485125
0.6842 Remote Similarity NPC486513
0.6839 Remote Similarity NPC485245
0.6704 Remote Similarity NPC479141
0.6686 Remote Similarity NPC482981
0.6667 Remote Similarity NPC329855
0.6667 Remote Similarity NPC486508
0.6648 Remote Similarity NPC484078
0.6576 Remote Similarity NPC489511
0.6552 Remote Similarity NPC480594
0.6505 Remote Similarity NPC329847
0.6484 Remote Similarity NPC484363
0.6477 Remote Similarity NPC320968
0.6343 Remote Similarity NPC481408
0.6283 Remote Similarity NPC479128
0.6237 Remote Similarity NPC484362
0.6117 Remote Similarity NPC480533
0.6114 Remote Similarity NPC489215
0.6054 Remote Similarity NPC489217
0.6038 Remote Similarity NPC480595
0.6023 Remote Similarity NPC485116
0.5897 Remote Similarity NPC489216
0.5891 Remote Similarity NPC486504
0.5885 Remote Similarity NPC479872
0.565 Remote Similarity NPC484874
0.5619 Remote Similarity NPC480596
0.5584 Remote Similarity NPC480440
0.5556 Remote Similarity NPC480529
0.5542 Remote Similarity NPC489555
0.5506 Remote Similarity NPC75634
0.5449 Remote Similarity NPC479574
0.5442 Remote Similarity NPC478504
0.5361 Remote Similarity NPC483985
0.5333 Remote Similarity NPC480528
0.5311 Remote Similarity NPC480530
0.5207 Remote Similarity NPC325976
0.5207 Remote Similarity NPC326363
0.5189 Remote Similarity NPC485242
0.5156 Remote Similarity NPC484364
0.5137 Remote Similarity NPC479131
0.5126 Remote Similarity NPC489225
0.5106 Remote Similarity NPC481409
0.5088 Remote Similarity NPC489549
0.508 Remote Similarity NPC329295
0.5079 Remote Similarity NPC153400

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC486514 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
0.5057 Remote Similarity NPD7970 Phase 4
0.5057 Remote Similarity NPD7971 Clinical (unspecified phase)

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