Natural Product: NPC484362

Natural Product IDNPC484362
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
RFWASKWFTRTSPX-FYSMNOCNSA-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 RFWASKWFTRTSPX-FYSMNOCNSA-N
Standard InCHI InChI=1S/C127H189N31O35S6/c1-12-68(9)103(154-96(164)52-130)125(190)135-70(11)105(170)149-88-59-198-199-64-95-136-85(56-159)115(180)150-90-61-195-197-63-92(151-117(182)87(58-161)148-109(174)78(41-42-100(168)169)137-97(165)53-133-107(88)172)121(186)156-101(66(5)6)123(188)145-82(48-72-30-19-15-20-31-72)112(177)141-79(46-65(3)4)106(171)132-54-98(166)138-89(118(183)144-83(49-73-32-21-16-22-33-73)114(179)157-104(69(10)13-2)126(191)158-45-27-36-93(158)122(187)134-55-99(167)153-95)60-194-196-62-91(152-124(189)102(67(7)8)155-110(175)77(35-24-26-44-129)139-116(181)86(57-160)147-108(173)76(140-119(90)184)34-23-25-43-128)120(185)143-81(50-74-37-39-75(162)40-38-74)111(176)142-80(47-71-28-17-14-18-29-71)113(178)146-84(127(192)193)51-94(131)163/h14-22,28-33,37-40,65-70,76-93,95,101-104,136,159-162H,12-13,23-27,34-36,41-64,128-130H2,1-11H3,(H2,131,163)(H,132,171)(H,133,172)(H,134,187)(H,135,190)(H,137,165)(H,138,166)(H,139,181)(H,140,184)(H,141,177)(H,142,176)(H,143,185)(H,144,183)(H,145,188)(H,146,178)(H,147,173)(H,148,174)(H,149,170)(H,150,180)(H,151,182)(H,152,189)(H,153,167)(H,154,164)(H,155,175)(H,156,186)(H,157,179)(H,168,169)(H,192,193)/t68-,69-,70-,76-,77-,78-,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91-,92-,93-,95+,101-,102-,103-,104-/m0/s1
SMILES CC[C@H](C)[C@@H](C(=N[C@@H](C)C(=N[C@H]1CSSC[C@@H]2N[C@@H](CO)C(=N[C@H]3CSSC[C@@H](C(=N[C@@H](C(C)C)C(=N[C@@H](Cc4ccccc4)C(=N[C@@H](CC(C)C)C(=NCC(=N[C@@H](CSSC[C@@H](C(=N[C@@H](Cc4ccc(cc4)O)C(=N[C@@H](Cc4ccccc4)C(=N[C@@H](CC(=N)O)C(=O)O)O)O)O)N=C([C@H](C(C)C)N=C([C@H](CCCCN)N=C([C@H](CO)N=C([C@H](CCCCN)N=C3O)O)O)O)O)C(=N[C@@H](Cc3ccccc3)C(=N[C@@H]([C@@H](C)CC)C(=O)N3CCC[C@H]3C(=NCC(=N2)O)O)O)O)O)O)O)O)O)N=C([C@H](CO)N=C([C@H](CCC(=O)O)N=C(CN=C1O)O)O)O)O)O)O)N=C(CN)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2900.23 Volume:   2788.212
?
Van der Waals volume.
Dense:   1.04 LogP:   -4.949
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.54
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.864
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The logarithm of aqueous solubility value.
Rotatable Bonds:   45.0 Rigid Bonds:   115.0
TPSA:   1124.75
?
Topological Polar Surface Area.
H-Bond Acceptor:   66.0
H-Bond Donor:   40.0 Rings:   9.0
Heavy Atoms:   72.0

MedChem Properties

QED Drug-Likeness Score:   0.006 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.774 Fsp3:   0.583
MCE-18:   291.144
?
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:   0.336
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.258
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.34
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.77 Promiscuous compounds:   0.219

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.193 MDCK Permeability:   -5.539
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):   0.999
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:   0.379
Plasma Protein Binding (PPB):   9.678% Volume Distribution (VD):   -0.589
Fu: 131.646%
?
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:   0.002 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.078 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):  -3.749 Half-life (T1/2):  9.888

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:  0.995
Maximum Recommended Daily Dose:  0.677 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.959
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.351 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.345
?
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:   3.441
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.731
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.22
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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
NPO31475 Palicourea rigida Species Rubiaceae Eukaryota n.a. root n.a. PMID[26927220]
NPO31475 Palicourea rigida Species Rubiaceae Eukaryota n.a. leaf n.a. PMID[26927220]
NPO31475 Palicourea rigida Species Rubiaceae Eukaryota n.a. flower n.a. PMID[26927220]
NPO31475 Palicourea rigida Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27809507]
NPO31475 Palicourea rigida Species Rubiaceae 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
NPT83 Cell line MCF7 Homo sapiens IC50 = 7770.0 nM PMID[27809507]

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 NPC484362 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
0.8092 Intermediate Similarity NPC485114
0.7669 Intermediate Similarity NPC482981
0.7118 Intermediate Similarity NPC484365
0.6941 Remote Similarity NPC477632
0.6941 Remote Similarity NPC486505
0.6882 Remote Similarity NPC486507
0.6882 Remote Similarity NPC485115
0.6591 Remote Similarity NPC484964
0.6536 Remote Similarity NPC484363
0.6484 Remote Similarity NPC486515
0.6463 Remote Similarity NPC485116
0.64 Remote Similarity NPC484963
0.6364 Remote Similarity NPC485246
0.6313 Remote Similarity NPC485243
0.6237 Remote Similarity NPC486506
0.6237 Remote Similarity NPC485247
0.6237 Remote Similarity NPC486514
0.6236 Remote Similarity NPC485245
0.6216 Remote Similarity NPC477635
0.6215 Remote Similarity NPC484364
0.6146 Remote Similarity NPC329843
0.6096 Remote Similarity NPC484965
0.6056 Remote Similarity NPC484078
0.599 Remote Similarity NPC486517
0.5846 Remote Similarity NPC477634
0.5795 Remote Similarity NPC477633
0.5744 Remote Similarity NPC485244
0.5674 Remote Similarity NPC485113
0.5637 Remote Similarity NPC479082
0.5628 Remote Similarity NPC480595
0.5585 Remote Similarity NPC489217
0.5539 Remote Similarity NPC479083
0.5519 Remote Similarity NPC486513
0.5365 Remote Similarity NPC479141
0.535 Remote Similarity NPC489215
0.5312 Remote Similarity NPC61004
0.5283 Remote Similarity NPC480596
0.5251 Remote Similarity NPC479131
0.5243 Remote Similarity NPC481408
0.5224 Remote Similarity NPC489216
0.5192 Remote Similarity NPC489512
0.5179 Remote Similarity NPC479140
0.515 Remote Similarity NPC480440
0.5137 Remote Similarity NPC479130
0.5137 Remote Similarity NPC485242
0.5137 Remote Similarity NPC479129
0.5084 Remote Similarity NPC482856

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484362 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