Natural Product: NPC486508

Natural Product IDNPC486508
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
JJTSSFQTAAWSTF-DXBOVLASSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 56666404
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 JJTSSFQTAAWSTF-DXBOVLASSA-N
Standard InCHI InChI=1S/C116H177N35O39S6/c1-49(2)31-64-113(188)149-28-17-23-75(149)105(180)144-86(51(5)6)108(183)138-68-43-191-192-44-69-99(174)135-67(42-153)98(173)137-70-45-193-195-47-72(141-112(187)90(55(11)156)146-95(170)61(25-26-84(165)166)128-80(161)38-125-93(68)168)102(177)143-85(50(3)4)107(182)127-36-79(160)123-37-83(164)142-88(53(9)154)110(185)140-71(100(175)133-63(34-78(118)159)96(171)148-91(56(12)157)115(190)151-30-16-22-74(151)104(179)126-40-82(163)130-69)46-194-196-48-73(103(178)147-89(54(10)155)111(186)131-60(21-15-27-121-116(119)120)94(169)132-62(33-77(117)158)92(167)124-39-81(162)129-64)139-109(184)87(52(7)8)145-106(181)76-24-18-29-150(76)114(189)65(134-97(172)66(41-152)136-101(70)176)32-57-35-122-59-20-14-13-19-58(57)59/h13-14,19-20,35,49-56,60-76,85-91,122,152-157H,15-18,21-34,36-48H2,1-12H3,(H2,117,158)(H2,118,159)(H,123,160)(H,124,167)(H,125,168)(H,126,179)(H,127,182)(H,128,161)(H,129,162)(H,130,163)(H,131,186)(H,132,169)(H,133,175)(H,134,172)(H,135,174)(H,136,176)(H,137,173)(H,138,183)(H,139,184)(H,140,185)(H,141,187)(H,142,164)(H,143,177)(H,144,180)(H,145,181)(H,146,170)(H,147,178)(H,148,171)(H,165,166)(H4,119,120,121)/t53-,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+,91+/m1/s1
SMILES CC(C)C[C@H]1C(=O)N2CCC[C@H]2C(=N[C@@H](C(C)C)C(=N[C@H]2CSSC[C@H]3C(=N[C@@H](CO)C(=N[C@H]4CSSC[C@@H](C(=N[C@@H](C(C)C)C(=NCC(=NCC(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CCCNC(=N)N)C(=N[C@@H](CC(=N)O)C(=NCC(=N1)O)O)O)O)O)N=C([C@H](C(C)C)N=C([C@@H]1CCCN1C(=O)[C@H](Cc1c[nH]c5ccccc15)N=C([C@H](CO)N=C4O)O)O)O)C(=N[C@@H](CC(=N)O)C(=N[C@@H]([C@@H](C)O)C(=O)N1CCC[C@H]1C(=NCC(=N3)O)O)O)O)O)O)O)O)O)N=C([C@H]([C@@H](C)O)N=C([C@H](CCC(=O)O)N=C(CN=C2O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2876.13 Volume:   2679.093
?
Van der Waals volume.
Dense:   1.074 LogP:   -8.832
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -5.643
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.896
?
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:   9.811 Fsp3:   0.647
MCE-18:   339.152
?
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:   0.361
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.339
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.376
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.756 Promiscuous compounds:   0.247

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.243 MDCK Permeability:   -5.269
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:   0.714
Plasma Protein Binding (PPB):   -28.271% Volume Distribution (VD):   -0.928
Fu: 157.883%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.008 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 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):  -4.247 Half-life (T1/2):  10.692

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:  0.445
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.999 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.005
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.999 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.309
?
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:   2.937
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.618
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.142
?
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
NPO40953 Viola tonkinensis Species Violaceae Eukaryota n.a. n.a. n.a. PMID[32437150]
NPO40951 Viola austrosinensis Species Violaceae Eukaryota n.a. n.a. n.a. PMID[32437150]
NPO40392 Viola arcuata Species Violaceae Eukaryota n.a. n.a. n.a. PMID[32437150]
NPO40392 Viola arcuata Species Violaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40951 Viola austrosinensis Species Violaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40953 Viola tonkinensis 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
NPT389 Cell line RPMI-8226 Homo sapiens IC50 = 2730.0 nM PMID[20718473]
NPT5192 Cell line U-937/GTB Homo sapiens IC50 = 2730.0 nM PMID[20718473]
NPT466 Cell line U-937 Homo sapiens IC50 = 2730.0 nM PMID[20718473]
NPT369 Cell line ACHN Homo sapiens IC50 = 2730.0 nM PMID[20718473]
NPT404 Cell line CCRF-CEM Homo sapiens IC50 = 2730.0 nM PMID[20718473]
NPT7275 Cell line R1 Mus musculus IC50 = 2730.0 nM PMID[20718473]
NPT306 Cell line PC-3 Homo sapiens IC50 = 3600.0 nM PMID[32437150]
NPT165 Cell line HeLa Homo sapiens IC50 = 5200.0 nM PMID[32437150]
NPT737 Cell line HUVEC Homo sapiens IC50 = 4000.0 nM PMID[32437150]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 2730.0 nM PMID[20718473]
NPT20950 Cell line Erythrocyte n.a. IC50 >= 50000.0 nM PMID[32437150]

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 NPC486508 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
0.9726 High Similarity NPC485125
0.9396 High Similarity NPC486503
0.8974 High Similarity NPC329847
0.8805 High Similarity NPC329855
0.7714 Intermediate Similarity NPC479083
0.7614 Intermediate Similarity NPC486504
0.7528 Intermediate Similarity NPC479082
0.6939 Remote Similarity NPC485124
0.6854 Remote Similarity NPC485244
0.6726 Remote Similarity NPC485246
0.6667 Remote Similarity NPC486506
0.6667 Remote Similarity NPC485247
0.6667 Remote Similarity NPC485243
0.6667 Remote Similarity NPC486514
0.6648 Remote Similarity NPC477635
0.6648 Remote Similarity NPC486515
0.6588 Remote Similarity NPC485245
0.6471 Remote Similarity NPC486517
0.6203 Remote Similarity NPC329843
0.6089 Remote Similarity NPC480594
0.5909 Remote Similarity NPC486507
0.5876 Remote Similarity NPC477632
0.5819 Remote Similarity NPC484963
0.5812 Remote Similarity NPC477634
0.5806 Remote Similarity NPC489511
0.5787 Remote Similarity NPC486505
0.5763 Remote Similarity NPC320968
0.5759 Remote Similarity NPC477633
0.5742 Remote Similarity NPC483985
0.5739 Remote Similarity NPC486513
0.5722 Remote Similarity NPC484965
0.5606 Remote Similarity NPC489512
0.5574 Remote Similarity NPC484964
0.547 Remote Similarity NPC485115
0.5351 Remote Similarity NPC484365
0.5255 Remote Similarity NPC489216
0.5243 Remote Similarity NPC484078
0.5131 Remote Similarity NPC489538
0.5098 Remote Similarity NPC155143
0.5054 Remote Similarity NPC484364

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC486508 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
0.559 Remote Similarity NPD7970 Phase 4
0.559 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