Natural Product: NPC479083

Natural Product IDNPC479083
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
NBLTXINQTJDPAB-PFJGMMEWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 46883522
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 NBLTXINQTJDPAB-PFJGMMEWSA-N
Standard InCHI InChI=1S/C134H207N41O42S6/c1-11-67(8)105-127(211)167-90(121(205)162-81(54-176)115(199)161-82(55-177)116(200)163-84(57-179)132(216)217)63-223-218-58-85-109(193)146-48-96(184)144-47-95(183)145-49-97(185)154-88-61-221-220-60-87(153-94(182)45-136)118(202)157-76(34-35-102(190)191)108(192)147-50-98(186)151-77(28-17-18-36-135)129(213)173-39-22-32-92(173)123(207)166-86(110(194)148-51-99(187)152-78(42-64(2)3)113(197)158-79(43-70-24-13-12-14-25-70)114(198)155-74(29-19-37-141-133(137)138)111(195)160-83(56-178)117(201)164-85)59-219-222-62-89(165-112(196)75(156-119(88)203)30-20-38-142-134(139)140)120(204)159-80(44-71-46-143-73-27-16-15-26-72(71)73)130(214)174-40-23-33-93(174)124(208)171-106(68(9)180)128(212)170-104(66(6)7)126(210)172-107(69(10)181)131(215)175-41-21-31-91(175)122(206)149-52-100(188)168-103(65(4)5)125(209)150-53-101(189)169-105/h12-16,24-27,46,64-69,74-93,103-107,143,176-181H,11,17-23,28-45,47-63,135-136H2,1-10H3,(H,144,184)(H,145,183)(H,146,193)(H,147,192)(H,148,194)(H,149,206)(H,150,209)(H,151,186)(H,152,187)(H,153,182)(H,154,185)(H,155,198)(H,156,203)(H,157,202)(H,158,197)(H,159,204)(H,160,195)(H,161,199)(H,162,205)(H,163,200)(H,164,201)(H,165,196)(H,166,207)(H,167,211)(H,168,188)(H,169,189)(H,170,212)(H,171,208)(H,172,210)(H,190,191)(H,216,217)(H4,137,138,141)(H4,139,140,142)/t67-,68+,69+,74-,75-,76-,77-,78-,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91-,92-,93-,103-,104-,105-,106-,107-/m0/s1
SMILES CC[C@H](C)[C@H]1C(=N[C@@H](CSSC[C@H]2C(=NCC(=NCC(=NCC(=N[C@H]3CSSC[C@@H](C(=N[C@@H](CCC(=O)O)C(=NCC(=N[C@@H](CCCCN)C(=O)N4CCC[C@H]4C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](Cc4c[nH]c5ccccc45)C(=O)N4CCC[C@H]4C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](C(C)C)C(=N[C@@H]([C@@H](C)O)C(=O)N4CCC[C@H]4C(=NCC(=N[C@@H](C(C)C)C(=NCC(=N1)O)O)O)O)O)O)O)O)N=C([C@H](CCCNC(=N)N)N=C3O)O)C(=NCC(=N[C@@H](CC(C)C)C(=N[C@@H](Cc1ccccc1)C(=N[C@@H](CCCNC(=N)N)C(=N[C@@H](CO)C(=N2)O)O)O)O)O)O)O)O)O)O)N=C(CN)O)O)O)O)O)C(=N[C@@H](CO)C(=N[C@@H](CO)C(=N[C@@H](CO)C(=O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   3254.36 Volume:   3066.953
?
Van der Waals volume.
Dense:   1.061 LogP:   -8.275
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.593
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -6.928
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   42.0 Rigid Bonds:   138.0
TPSA:   1393.65
?
Topological Polar Surface Area.
H-Bond Acceptor:   83.0
H-Bond Donor:   50.0 Rings:   9.0
Heavy Atoms:   89.0

MedChem Properties

QED Drug-Likeness Score:   0.009 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.96 Fsp3:   0.627
MCE-18:   343.771
?
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:   0.353
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.336
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.334
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.79 Promiscuous compounds:   0.216

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.284 MDCK Permeability:   -5.448
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:   0.984
Plasma Protein Binding (PPB):   -40.396% Volume Distribution (VD):   -1.024
Fu: 250.009%
?
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:   0.994 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):  -4.488 Half-life (T1/2):  10.979

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:  0.642
Maximum Recommended Daily Dose:  0.014 Skin Sensitization:  1.0
Carcinogencity:  0.955 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.878
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.157 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.39
?
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:   3.037
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.615
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.144
?
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
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota Seeds n.a. n.a. PMID[19711988]
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19870 Momordica cochinchinensis Species Cucurbitaceae Eukaryota 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

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1524 Cell line MM96L Homo sapiens Survival = 51.0 % PMID[19711988]
NPT1523 Cell line NFF Homo sapiens Survival = 86.0 % PMID[19711988]





 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 NPC479083 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
0.9651 High Similarity NPC479082
0.8156 Intermediate Similarity NPC329855
0.7989 Intermediate Similarity NPC329847
0.7943 Intermediate Similarity NPC485125
0.7714 Intermediate Similarity NPC486508
0.7697 Intermediate Similarity NPC486503
0.7306 Intermediate Similarity NPC486517
0.7166 Intermediate Similarity NPC486506
0.7166 Intermediate Similarity NPC485247
0.7166 Intermediate Similarity NPC486514
0.7158 Intermediate Similarity NPC485244
0.7151 Intermediate Similarity NPC477635
0.7135 Intermediate Similarity NPC329843
0.7059 Intermediate Similarity NPC486515
0.7056 Intermediate Similarity NPC485246
0.6902 Remote Similarity NPC485243
0.6831 Remote Similarity NPC485245
0.6813 Remote Similarity NPC486507
0.68 Remote Similarity NPC486504
0.6635 Remote Similarity NPC480594
0.6578 Remote Similarity NPC484365
0.6505 Remote Similarity NPC477632
0.6486 Remote Similarity NPC320968
0.6452 Remote Similarity NPC485115
0.6417 Remote Similarity NPC486505
0.64 Remote Similarity NPC477634
0.6378 Remote Similarity NPC486513
0.635 Remote Similarity NPC477633
0.6327 Remote Similarity NPC489511
0.6262 Remote Similarity NPC489512
0.6244 Remote Similarity NPC484965
0.6198 Remote Similarity NPC484964
0.619 Remote Similarity NPC484963
0.6082 Remote Similarity NPC489217
0.6073 Remote Similarity NPC482981
0.5892 Remote Similarity NPC485114
0.5855 Remote Similarity NPC484364
0.5845 Remote Similarity NPC480533
0.5815 Remote Similarity NPC75634
0.5795 Remote Similarity NPC484078
0.5639 Remote Similarity NPC480595
0.5622 Remote Similarity NPC479141
0.5615 Remote Similarity NPC484874
0.5598 Remote Similarity NPC479128
0.5539 Remote Similarity NPC484362
0.552 Remote Similarity NPC480596
0.5438 Remote Similarity NPC480530
0.5422 Remote Similarity NPC479872
0.5403 Remote Similarity NPC489216
0.5361 Remote Similarity NPC485113
0.5318 Remote Similarity NPC480529
0.5318 Remote Similarity NPC480528
0.5305 Remote Similarity NPC489215
0.5291 Remote Similarity NPC484363
0.5279 Remote Similarity NPC481408
0.5278 Remote Similarity NPC485124
0.5261 Remote Similarity NPC480440
0.5258 Remote Similarity NPC485242
0.5211 Remote Similarity NPC485116
0.5169 Remote Similarity NPC483985
0.5167 Remote Similarity NPC479574
0.5087 Remote Similarity NPC478504

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC479083 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