Natural Product: NPC480939

Natural Product IDNPC480939
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZBUMKOQYNCYXMY-NLYCDFQESA-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 ZBUMKOQYNCYXMY-NLYCDFQESA-N
Standard InCHI InChI=1S/C54H84O25/c1-49(2)14-15-54(48(70)71)22(16-49)21-8-9-27-51(5)12-11-29(50(3,4)26(51)10-13-52(27,6)53(21,7)17-28(54)58)75-47-42(79-45-37(66)34(63)31(60)24(19-56)73-45)39(38(67)40(77-47)43(68)69)76-46-41(35(64)32(61)25(20-57)74-46)78-44-36(65)33(62)30(59)23(18-55)72-44/h8,22-27,29-42,44-47,55-57,59-67H,9-20H2,1-7H3,(H,68,69)(H,70,71)/t22-,23+,24-,25+,26-,27+,29-,30+,31-,32+,33-,34+,35-,36+,37-,38-,39-,40-,41+,42+,44-,45+,46-,47+,51-,52+,53+,54+/m0/s1
SMILES CC1(C)CC[C@]2([C@@H](C1)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)CC2=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1132.53 Volume:   1074.741
?
Van der Waals volume.
Dense:   1.054 LogP:   -0.584
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.003
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.251
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   53.0
TPSA:   408.27
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   14.0 Rings:   9.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.053 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.943 Fsp3:   0.907
MCE-18:   201.282
?
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:   0.909 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.007
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.302 Promiscuous compounds:   0.163

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.832 MDCK Permeability:   -4.992
Pgp-inhibitor:   0.0 Pgp-substrate:   0.002
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):   0.978
20% Bioavailability (F20%):   0.022 30% Bioavailability (F30%):   0.95
50% Bioavailability (F50%):   0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.736
Plasma Protein Binding (PPB):   69.986% Volume Distribution (VD):   -0.483
Fu: 18.685%
?
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:   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):  -0.571 Half-life (T1/2):  4.082

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.785 Drug-induced Liver Injury (DILI):  0.994
AMES Toxicity:  0.857 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.035 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.534 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.839 RPMI-8226 Immunitoxicity:  0.068
A549 Cytotoxicity:  0.072 Hek293 Cytotoxicity:  0.017
BCF:   0.454
?
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:   3.293
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.911
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.821
?
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
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[39065796]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23380 Camellia japonica Species Theaceae 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
NPT804 Cell line HT-22 Mus musculus Activity = 61.7 % PMID[32569471]

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 NPC480939 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
0.7573 Intermediate Similarity NPC22956
0.7523 Intermediate Similarity NPC469947
0.7523 Intermediate Similarity NPC480948
0.7273 Intermediate Similarity NPC160452
0.7157 Intermediate Similarity NPC164194
0.7156 Intermediate Similarity NPC302887
0.7027 Intermediate Similarity NPC23275
0.6949 Remote Similarity NPC181066
0.6893 Remote Similarity NPC480938
0.6822 Remote Similarity NPC472949
0.6792 Remote Similarity NPC25605
0.6636 Remote Similarity NPC114304
0.6577 Remote Similarity NPC44716
0.6574 Remote Similarity NPC127056
0.6574 Remote Similarity NPC109079
0.6514 Remote Similarity NPC488561
0.6475 Remote Similarity NPC484061
0.6475 Remote Similarity NPC484062
0.6455 Remote Similarity NPC80843
0.6446 Remote Similarity NPC277212
0.6446 Remote Similarity NPC30279
0.6372 Remote Similarity NPC475591
0.6372 Remote Similarity NPC236870
0.6371 Remote Similarity NPC225791
0.632 Remote Similarity NPC484059
0.632 Remote Similarity NPC484060
0.6271 Remote Similarity NPC480936
0.6261 Remote Similarity NPC79718
0.625 Remote Similarity NPC484063
0.625 Remote Similarity NPC484064
0.6239 Remote Similarity NPC12288
0.6214 Remote Similarity NPC606107
0.6195 Remote Similarity NPC480947
0.6179 Remote Similarity NPC46823
0.6098 Remote Similarity NPC283417
0.6098 Remote Similarity NPC200049
0.6095 Remote Similarity NPC31839
0.6083 Remote Similarity NPC288205
0.6083 Remote Similarity NPC51465
0.6071 Remote Similarity NPC603026
0.6053 Remote Similarity NPC605226
0.605 Remote Similarity NPC187290
0.6036 Remote Similarity NPC59804
0.6017 Remote Similarity NPC324875
0.6017 Remote Similarity NPC292677
0.5917 Remote Similarity NPC475486
0.5906 Remote Similarity NPC265841
0.5897 Remote Similarity NPC257468
0.5893 Remote Similarity NPC56713
0.5873 Remote Similarity NPC71391
0.5868 Remote Similarity NPC62725
0.5833 Remote Similarity NPC488564
0.5781 Remote Similarity NPC488308
0.576 Remote Similarity NPC251263
0.5736 Remote Similarity NPC312650
0.5726 Remote Similarity NPC251768
0.5691 Remote Similarity NPC25998
0.569 Remote Similarity NPC469945
0.5669 Remote Similarity NPC47995
0.566 Remote Similarity NPC204407
0.5656 Remote Similarity NPC329976
0.5645 Remote Similarity NPC609119
0.5639 Remote Similarity NPC488309
0.5635 Remote Similarity NPC219180
0.5625 Remote Similarity NPC192765
0.5615 Remote Similarity NPC271610
0.561 Remote Similarity NPC605294
0.5593 Remote Similarity NPC180550
0.5593 Remote Similarity NPC35405
0.5583 Remote Similarity NPC64715
0.5581 Remote Similarity NPC178264
0.5565 Remote Similarity NPC114441
0.5556 Remote Similarity NPC192791
0.5547 Remote Similarity NPC473918
0.5537 Remote Similarity NPC276093
0.5512 Remote Similarity NPC166422
0.5505 Remote Similarity NPC286347
0.5492 Remote Similarity NPC301449
0.5492 Remote Similarity NPC291903
0.5492 Remote Similarity NPC601290
0.5489 Remote Similarity NPC302543
0.5478 Remote Similarity NPC174679
0.5478 Remote Similarity NPC279554
0.5469 Remote Similarity NPC602995
0.5462 Remote Similarity NPC104400
0.5462 Remote Similarity NPC10320
0.5455 Remote Similarity NPC488515
0.5455 Remote Similarity NPC119794
0.5447 Remote Similarity NPC120116
0.5446 Remote Similarity NPC191410
0.544 Remote Similarity NPC475119
0.5433 Remote Similarity NPC284449
0.5426 Remote Similarity NPC54636
0.5417 Remote Similarity NPC139044
0.5417 Remote Similarity NPC118440
0.541 Remote Similarity NPC114692
0.5385 Remote Similarity NPC329828
0.5372 Remote Similarity NPC131469
0.5366 Remote Similarity NPC323359
0.5351 Remote Similarity NPC270667
0.5351 Remote Similarity NPC76999
0.5339 Remote Similarity NPC469946
0.5338 Remote Similarity NPC476779
0.5328 Remote Similarity NPC95437
0.5312 Remote Similarity NPC133818
0.5276 Remote Similarity NPC313110
0.5276 Remote Similarity NPC473824
0.5259 Remote Similarity NPC136877
0.5254 Remote Similarity NPC6377
0.5254 Remote Similarity NPC208381
0.5254 Remote Similarity NPC488516
0.5246 Remote Similarity NPC481082
0.5246 Remote Similarity NPC164419
0.5234 Remote Similarity NPC151543
0.5227 Remote Similarity NPC21691
0.5207 Remote Similarity NPC159309
0.5207 Remote Similarity NPC480475
0.5207 Remote Similarity NPC86222
0.5197 Remote Similarity NPC470475
0.5194 Remote Similarity NPC477465
0.5188 Remote Similarity NPC476774
0.5188 Remote Similarity NPC476780
0.5185 Remote Similarity NPC110700
0.5185 Remote Similarity NPC111466
0.5182 Remote Similarity NPC283849
0.5179 Remote Similarity NPC242611
0.5161 Remote Similarity NPC236657
0.5152 Remote Similarity NPC4749
0.513 Remote Similarity NPC475472
0.5126 Remote Similarity NPC157868
0.5122 Remote Similarity NPC470514
0.5113 Remote Similarity NPC470518
0.5111 Remote Similarity NPC161717
0.5088 Remote Similarity NPC480937
0.5085 Remote Similarity NPC309780
0.5083 Remote Similarity NPC213674
0.5079 Remote Similarity NPC187618
0.5078 Remote Similarity NPC476992
0.5077 Remote Similarity NPC323341
0.5074 Remote Similarity NPC476777
0.5041 Remote Similarity NPC112352
0.504 Remote Similarity NPC114484
0.5039 Remote Similarity NPC609281
0.5038 Remote Similarity NPC470476
0.5037 Remote Similarity NPC258617
0.5036 Remote Similarity NPC279915

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480939 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