Natural Product: NPC480913

Natural Product IDNPC480913
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
DFJGFVMDWLNMQU-CZJBNPPGSA-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 DFJGFVMDWLNMQU-CZJBNPPGSA-N
Standard InCHI InChI=1S/C23H34O6/c1-21-6-4-16-17(3-2-14-9-18(25)19(26)10-22(14,16)12-24)23(21,28)7-5-15(21)13-8-20(27)29-11-13/h8,14-19,24-26,28H,2-7,9-12H2,1H3/t14-,15-,16+,17-,18-,19-,21-,22-,23+/m1/s1
SMILES C[C@@]12CC[C@H]3[C@@H](CC[C@@H]4C[C@H]([C@@H](C[C@]34CO)O)O)[C@]2(CC[C@@H]1C1=CC(=O)OC1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   406.24 Volume:   411.05
?
Van der Waals volume.
Dense:   0.988 LogP:   1.254
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.824
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.504
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The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   26.0
TPSA:   107.22
?
Topological Polar Surface Area.
H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   5.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.519 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.858 Fsp3:   0.87
MCE-18:   90.791
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.512 Fluc inhibitor:   0.158
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.019
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.266 Promiscuous compounds:   0.532

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.219 MDCK Permeability:   -4.806
Pgp-inhibitor:   0.008 Pgp-substrate:   0.912
PAMPA:   0.97
?
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):   0.031
20% Bioavailability (F20%):   0.645 30% Bioavailability (F30%):   0.506
50% Bioavailability (F50%):   0.883

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.386 MRP1:   0.891
Plasma Protein Binding (PPB):   73.06% Volume Distribution (VD):   0.092
Fu: 27.75%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.931
OATP1B3 inhibitor:   0.97 BCRP inhibitor:   0.006
BSEP inhibitor:   0.451

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.023 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.763
HLM stability:   0.065
?
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):  4.794 Half-life (T1/2):  2.681

ADMET: Toxicity

hERG Blockers:  0.072 hERG Blockers (10um):  0.289
Human Hepatotoxicity (H-HT):  0.671 Drug-induced Liver Injury (DILI):  0.203
AMES Toxicity:  0.796 Rat Oral Acute Toxicity:  0.471
Maximum Recommended Daily Dose:  0.941 Skin Sensitization:  0.998
Carcinogencity:  0.939 Eye Corrosion:  0.0
Eye Irritation:  0.045 Respiratory Toxicity:  0.555
Drug-induced Neurotoxicity:  0.061 Ototoxicity:  0.808
Hematotoxicity:  0.682 Drug-induced Nephrotoxicity:  0.937
Genotoxicity:  0.762 RPMI-8226 Immunitoxicity:  0.324
A549 Cytotoxicity:  0.512 Hek293 Cytotoxicity:  0.712
BCF:   0.479
?
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:   3.219
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.854
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.876
?
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
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota leaves n.a. n.a. PMID[16933890]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. root n.a. PMID[19052526]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28817274]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[31967821]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[32649211]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[9548837]
NPO30295 Calotropis gigantea Species Apocynaceae 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
NPT461 Cell line PANC-1 Homo sapiens IC50 = 5100.0 nM PMID[31967821]
NPT165 Cell line HeLa Homo sapiens IC50 > 10000.0 nM PMID[31967821]

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 NPC480913 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
0.7869 Intermediate Similarity NPC222875
0.7869 Intermediate Similarity NPC25177
0.7705 Intermediate Similarity NPC196931
0.6984 Remote Similarity NPC187302
0.6719 Remote Similarity NPC268829
0.6719 Remote Similarity NPC295110
0.6119 Remote Similarity NPC10232
0.6087 Remote Similarity NPC196471
0.5974 Remote Similarity NPC77299
0.5974 Remote Similarity NPC480906
0.597 Remote Similarity NPC186668
0.5897 Remote Similarity NPC76572
0.5897 Remote Similarity NPC193382
0.5821 Remote Similarity NPC97487
0.5797 Remote Similarity NPC480911
0.575 Remote Similarity NPC483822
0.575 Remote Similarity NPC305574
0.5652 Remote Similarity NPC160583
0.561 Remote Similarity NPC329905
0.5571 Remote Similarity NPC72772
0.557 Remote Similarity NPC5311
0.5513 Remote Similarity NPC473852
0.5513 Remote Similarity NPC471633
0.55 Remote Similarity NPC480914
0.5429 Remote Similarity NPC189588
0.5412 Remote Similarity NPC32177
0.5412 Remote Similarity NPC469756
0.5412 Remote Similarity NPC275901
0.5362 Remote Similarity NPC220217
0.5349 Remote Similarity NPC480910
0.5349 Remote Similarity NPC480909
0.5316 Remote Similarity NPC99620
0.525 Remote Similarity NPC196429
0.5238 Remote Similarity NPC480907
0.5227 Remote Similarity NPC486135
0.5227 Remote Similarity NPC486137
0.5185 Remote Similarity NPC469750
0.5185 Remote Similarity NPC480915
0.5122 Remote Similarity NPC199428
0.5122 Remote Similarity NPC243196
0.5122 Remote Similarity NPC84949
0.5122 Remote Similarity NPC109448
0.5122 Remote Similarity NPC480562
0.5122 Remote Similarity NPC74945
0.5122 Remote Similarity NPC310341
0.5122 Remote Similarity NPC31354
0.5122 Remote Similarity NPC69576
0.5116 Remote Similarity NPC30483
0.5116 Remote Similarity NPC470897
0.5067 Remote Similarity NPC475030
0.5062 Remote Similarity NPC84987
0.506 Remote Similarity NPC253456
0.506 Remote Similarity NPC159338
0.506 Remote Similarity NPC88668
0.506 Remote Similarity NPC250556
0.5059 Remote Similarity NPC72260
0.5059 Remote Similarity NPC488161
0.5059 Remote Similarity NPC16569
0.5057 Remote Similarity NPC236973
0.5057 Remote Similarity NPC292467

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480913 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
0.506 Remote Similarity NPD7507 Pre-clinical
0.5059 Remote Similarity NPD8294 Phase 4

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