Natural Product: NPC477636

Natural Product IDNPC477636
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Cycloviolin A
IUPAC Name (1R,7S,12S,15R,18S,21S,24S,30S,33R,36S,39S,42S,45S,48S,54R,57S,60R,63S,66S,69S,72S,75S,78S,81S,84S,90S,93S,99S)-63,69-bis(4-aminobutyl)-66,84-bis(2-amino-2-oxoethyl)-21-benzyl-24,36,48,93-tetrakis[(2S)-butan-2-yl]-81-(3-carbamimidamidopropyl)-12,39,57-tris(hydroxymethyl)-78-[(4-hydroxyphenyl)methyl]-42,45-dimethyl-a,2,5,10,13,16,19,22,25,31,34,37,40,43,46,49,52,55,58,61,64,67,70,73,76,79,82,85,88,91,94-hentriacontaoxo-18,72,90-tri(propan-2-yl)-3a,4a,7a,8a,11a,12a-hexathia-1a,3,6,11,14,17,20,23,26,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80,83,86,89,92,95-hentriacontazahexacyclo[52.47.4.415,60.433,75.026,30.095,99]tridecahectane-7-carboxylic acid
Synonyms Cycloviolin A
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44592645
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 WVDDKBIDSUUCLT-AWZLLTDASA-N
Standard InCHI InChI=1S/C137H216N38O39S6/c1-17-68(11)105-129(206)147-54-100(184)152-89-60-216-215-59-88-112(189)146-53-99(183)150-80(136(213)214)42-43-98(182)151-85(56-176)120(197)163-92-63-219-217-61-90(162-121(198)87(58-178)160-122(89)199)123(200)155-77(33-24-26-44-138)113(190)158-84(52-97(141)181)117(194)153-78(34-25-27-45-139)115(192)168-104(67(9)10)131(208)166-91(124(201)156-81(50-75-38-40-76(179)41-39-75)116(193)154-79(35-28-46-144-137(142)143)114(191)157-83(51-96(140)180)111(188)145-55-101(185)167-102(65(5)6)132(209)173-108(71(14)20-4)135(212)175-48-29-36-94(175)127(204)164-88)62-218-220-64-93(126(203)171-106(69(12)18-2)133(210)161-86(57-177)119(196)149-72(15)109(186)148-73(16)110(187)170-105)165-128(205)95-37-30-47-174(95)134(211)107(70(13)19-3)172-118(195)82(49-74-31-22-21-23-32-74)159-130(207)103(66(7)8)169-125(92)202/h21-23,31-32,38-41,65-73,77-95,102-108,176-179H,17-20,24-30,33-37,42-64,138-139H2,1-16H3,(H2,140,180)(H2,141,181)(H,145,188)(H,146,189)(H,147,206)(H,148,186)(H,149,196)(H,150,183)(H,151,182)(H,152,184)(H,153,194)(H,154,193)(H,155,200)(H,156,201)(H,157,191)(H,158,190)(H,159,207)(H,160,199)(H,161,210)(H,162,198)(H,163,197)(H,164,204)(H,165,205)(H,166,208)(H,167,185)(H,168,192)(H,169,202)(H,170,187)(H,171,203)(H,172,195)(H,173,209)(H,213,214)(H4,142,143,144)/t68-,69-,70-,71-,72-,73-,77-,78-,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91+,92-,93-,94-,95-,102-,103-,104-,105-,106-,107-,108-/m0/s1
SMILES CC[C@H](C)[C@H]1C(=O)NCC(=O)N[C@H]2CSSC[C@H]3C(=O)NCC(=O)N[C@@H](CCC(=O)N[C@H](C(=O)N[C@H]4CSSC[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](CSSC[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1)C)C)CO)[C@@H](C)CC)NC(=O)[C@@H]5CCCN5C(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC4=O)C(C)C)CC6=CC=CC=C6)[C@@H](C)CC)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N7CCC[C@H]7C(=O)N3)[C@@H](C)CC)C(C)C)CC(=O)N)CCCNC(=N)N)CC8=CC=C(C=C8)O)C(C)C)CCCCN)CC(=O)N)CCCCN)NC(=O)[C@@H](NC2=O)CO)CO)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   3209.44 Volume:   3073.31
?
Van der Waals volume.
Dense:   1.044 LogP:   -1.242
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.106
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.179
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The logarithm of aqueous solubility value.
Rotatable Bonds:   36.0 Rigid Bonds:   165.0
TPSA:   1202.86
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Topological Polar Surface Area.
H-Bond Acceptor:   77.0
H-Bond Donor:   46.0 Rings:   9.0
Heavy Atoms:   83.0

MedChem Properties

QED Drug-Likeness Score:   0.01 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.792 Fsp3:   0.657
MCE-18:   336.251
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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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.66 Fluc inhibitor:   0.157
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.334
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.667
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.794 Promiscuous compounds:   0.029

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.37 MDCK Permeability:   -5.202
Pgp-inhibitor:   1.0 Pgp-substrate:   0.512
PAMPA:   0.979
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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:   0.004
Plasma Protein Binding (PPB):   -44.293% Volume Distribution (VD):   -0.878
Fu: 238.908%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 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):  -0.9 Half-life (T1/2):  10.04

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.0 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.0 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  1.0 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.05
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   0.158
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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:   2.603
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.945
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.446
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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
NPO33585 Palicourea condensata Species Rubiaceae Eukaryota Bark Pastaza, Ecuador 1988-MAR PMID[11430013]
NPO33585 Palicourea condensata 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
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 EC50 = 50 nM PMID[11430013]

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 NPC477636 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
0.8243 Intermediate Similarity NPC477639
0.8182 Intermediate Similarity NPC600735
0.8013 Intermediate Similarity NPC477631
0.7867 Intermediate Similarity NPC609634
0.7843 Intermediate Similarity NPC477638
0.7548 Intermediate Similarity NPC610535
0.7391 Intermediate Similarity NPC600998
0.7391 Intermediate Similarity NPC611186
0.7329 Intermediate Similarity NPC610649
0.7284 Intermediate Similarity NPC610817
0.7195 Intermediate Similarity NPC477630
0.7013 Intermediate Similarity NPC603072
0.6883 Remote Similarity NPC604370
0.6883 Remote Similarity NPC610870
0.6832 Remote Similarity NPC608521
0.6731 Remote Similarity NPC606505
0.6667 Remote Similarity NPC477637
0.6584 Remote Similarity NPC607485
0.6467 Remote Similarity NPC601264
0.6265 Remote Similarity NPC610952
0.6117 Remote Similarity NPC607866
0.6095 Remote Similarity NPC609988
0.6061 Remote Similarity NPC600580
0.6061 Remote Similarity NPC605764
0.6061 Remote Similarity NPC605765
0.6 Remote Similarity NPC605666
0.6 Remote Similarity NPC607892
0.5989 Remote Similarity NPC610704
0.5833 Remote Similarity NPC611556
0.559 Remote Similarity NPC603135
0.5275 Remote Similarity NPC605177
0.5246 Remote Similarity NPC611013
0.5174 Remote Similarity NPC608676
0.517 Remote Similarity NPC601582
0.517 Remote Similarity NPC603992
0.517 Remote Similarity NPC610984
0.5055 Remote Similarity NPC600008
0.5055 Remote Similarity NPC600634
0.5055 Remote Similarity NPC603103
0.5055 Remote Similarity NPC604252

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC477636 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