Natural Product: NPC486503

Natural Product IDNPC486503
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
JRQOVZFYMIMYDG-KAIQXEDGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 52952313
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 JRQOVZFYMIMYDG-KAIQXEDGSA-N
Standard InCHI InChI=1S/C115H175N35O39S6/c1-12-51(6)86-108(183)139-73-48-195-194-47-72-101(176)133-63(34-78(117)158)96(171)147-90(56(11)156)114(189)150-30-16-22-74(150)104(179)126-40-82(162)130-69-44-191-190-43-68(138-107(182)85(50(4)5)143-105(180)75-23-17-28-148(75)112(187)64(31-49(2)3)129-81(161)39-124-92(167)62(33-77(116)157)132-94(169)60(21-15-27-120-115(118)119)131-110(185)88(54(9)154)146-103(73)178)93(168)125-38-80(160)128-61(25-26-84(164)165)95(170)145-89(55(10)155)111(186)140-70(99(174)127-52(7)91(166)123-36-79(159)122-37-83(163)142-87(53(8)153)109(184)141-72)45-192-193-46-71(137-98(173)67(42-152)135-100(69)175)102(177)136-66(41-151)97(172)134-65(32-57-35-121-59-20-14-13-19-58(57)59)113(188)149-29-18-24-76(149)106(181)144-86/h13-14,19-20,35,49-56,60-76,85-90,121,151-156H,12,15-18,21-34,36-48H2,1-11H3,(H2,116,157)(H2,117,158)(H,122,159)(H,123,166)(H,124,167)(H,125,168)(H,126,179)(H,127,174)(H,128,160)(H,129,161)(H,130,162)(H,131,185)(H,132,169)(H,133,176)(H,134,172)(H,135,175)(H,136,177)(H,137,173)(H,138,182)(H,139,183)(H,140,186)(H,141,184)(H,142,163)(H,143,180)(H,144,181)(H,145,170)(H,146,178)(H,147,171)(H,164,165)(H4,118,119,120)/t51-,52-,53+,54+,55+,56+,60-,61-,62-,63-,64-,65-,66-,67-,68-,69-,70-,71-,72-,73-,74-,75-,76-,85-,86-,87-,88-,89-,90-/m0/s1
SMILES CC[C@H](C)[C@H]1C(=N[C@H]2CSSC[C@H]3C(=N[C@@H](CC(=N)O)C(=N[C@@H]([C@@H](C)O)C(=O)N4CCC[C@H]4C(=NCC(=N[C@H]4CSSC[C@@H](C(=NCC(=N[C@@H](CCC(=O)O)C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](CO)C(=N[C@@H](Cc5c[nH]c6ccccc56)C(=O)N5CCC[C@H]5C(=N1)O)O)O)N=C([C@H](CO)N=C4O)O)C(=N[C@@H](C)C(=NCC(=NCC(=N[C@@H]([C@@H](C)O)C(=N3)O)O)O)O)O)O)O)O)O)N=C([C@H](C(C)C)N=C([C@@H]1CCCN1C(=O)[C@H](CC(C)C)N=C(CN=C([C@H](CC(=N)O)N=C([C@H](CCCNC(=N)N)N=C([C@H]([C@@H](C)O)N=C2O)O)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2862.11 Volume:   2661.797
?
Van der Waals volume.
Dense:   1.075 LogP:   -8.439
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -4.974
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.379
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   25.0 Rigid Bonds:   131.0
TPSA:   1232.8
?
Topological Polar Surface Area.
H-Bond Acceptor:   74.0
H-Bond Donor:   42.0 Rings:   10.0
Heavy Atoms:   80.0

MedChem Properties

QED Drug-Likeness Score:   0.017 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.817 Fsp3:   0.643
MCE-18:   336.164
?
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:   0.356
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.341
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.339
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.752 Promiscuous compounds:   0.244

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.287 MDCK Permeability:   -5.248
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:   0.997
Plasma Protein Binding (PPB):   -24.727% Volume Distribution (VD):   -0.887
Fu: 159.512%
?
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:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 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):  -4.326 Half-life (T1/2):  10.799

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:  0.272
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.998 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.004
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.998 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.303
?
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:   2.903
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.583
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.134
?
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
NPO30114 Viola abyssinica Species Violaceae Eukaryota n.a. n.a. n.a. PMID[21434649]
NPO30114 Viola abyssinica Species Violaceae Eukaryota n.a. aerial part n.a. PMID[21434649]
NPO30114 Viola abyssinica 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
NPT5192 Cell line U-937/GTB Homo sapiens IC50 = 7600.0 nM PMID[21434649]

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 NPC486503 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
0.9664 High Similarity NPC485125
0.9396 High Similarity NPC486508
0.8765 High Similarity NPC329855
0.858 High Similarity NPC329847
0.7697 Intermediate Similarity NPC479083
0.7514 Intermediate Similarity NPC479082
0.75 Intermediate Similarity NPC486504
0.7039 Intermediate Similarity NPC485244
0.6949 Remote Similarity NPC486506
0.6949 Remote Similarity NPC485247
0.6949 Remote Similarity NPC486514
0.6932 Remote Similarity NPC477635
0.6932 Remote Similarity NPC486515
0.6824 Remote Similarity NPC485246
0.6784 Remote Similarity NPC485245
0.6763 Remote Similarity NPC485243
0.6738 Remote Similarity NPC486517
0.6494 Remote Similarity NPC485124
0.6471 Remote Similarity NPC329843
0.625 Remote Similarity NPC477632
0.6193 Remote Similarity NPC484963
0.6176 Remote Similarity NPC480594
0.6162 Remote Similarity NPC489511
0.6158 Remote Similarity NPC486505
0.6011 Remote Similarity NPC486507
0.5989 Remote Similarity NPC484965
0.5955 Remote Similarity NPC320968
0.5939 Remote Similarity NPC489512
0.5934 Remote Similarity NPC484964
0.5855 Remote Similarity NPC477633
0.5843 Remote Similarity NPC486513
0.5744 Remote Similarity NPC477634
0.566 Remote Similarity NPC483985
0.5574 Remote Similarity NPC485115
0.5514 Remote Similarity NPC484078
0.5455 Remote Similarity NPC484365
0.5337 Remote Similarity NPC485114
0.5276 Remote Similarity NPC489216
0.5234 Remote Similarity NPC480533
0.5226 Remote Similarity NPC155143
0.5213 Remote Similarity NPC482981
0.5135 Remote Similarity NPC481408
0.5115 Remote Similarity NPC486283
0.5113 Remote Similarity NPC480595
0.5099 Remote Similarity NPC479128
0.5079 Remote Similarity NPC484364
0.5077 Remote Similarity NPC489538
0.5026 Remote Similarity NPC479141
0.5025 Remote Similarity NPC489215

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC486503 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
0.5515 Remote Similarity NPD7970 Phase 4
0.5515 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