Natural Product: NPC299488

Natural Product IDNPC299488
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YIMHGPSYDOGBPI-IQQSWPBXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6918114
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 YIMHGPSYDOGBPI-IQQSWPBXSA-N
Standard InCHI InChI=1S/C30H46O4/c1-17-8-11-26(3)14-15-28(5)19(23(26)18(17)2)16-20(31)24-27(4)12-10-22(32)30(7,25(33)34)21(27)9-13-29(24,28)6/h16-18,21-24,32H,8-15H2,1-7H3,(H,33,34)/t17-,18+,21?,22-,23?,24?,26-,27+,28-,29-,30-/m1/s1
SMILES C[C@@H]1CC[C@]2(C)CC[C@]3(C)C(=CC(=O)C4[C@@]5(C)CC[C@H]([C@@](C)(C5CC[C@@]34C)C(=O)O)O)C2[C@H]1C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   470.34 Volume:   511.905
?
Van der Waals volume.
Dense:   0.919 LogP:   3.51
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.011
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.248
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   28.0
TPSA:   74.6
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Topological Polar Surface Area.
H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.474 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.939 Fsp3:   0.867
MCE-18:   104.464
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.486 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.189
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.035
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.254 Promiscuous compounds:   0.17

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.561 MDCK Permeability:   -5.028
Pgp-inhibitor:   0.34 Pgp-substrate:   0.028
PAMPA:   0.986
?
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):   0.0
20% Bioavailability (F20%):   0.161 30% Bioavailability (F30%):   0.017
50% Bioavailability (F50%):   0.873

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.379 MRP1:   0.996
Plasma Protein Binding (PPB):   96.627% Volume Distribution (VD):   -0.477
Fu: 4.123%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.996 BCRP inhibitor:   0.091
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.005 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.087 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.187 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   0.005
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.07
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):  6.074 Half-life (T1/2):  0.965

ADMET: Toxicity

hERG Blockers:  0.031 hERG Blockers (10um):  0.114
Human Hepatotoxicity (H-HT):  0.83 Drug-induced Liver Injury (DILI):  0.298
AMES Toxicity:  0.148 Rat Oral Acute Toxicity:  0.415
Maximum Recommended Daily Dose:  0.441 Skin Sensitization:  0.715
Carcinogencity:  0.949 Eye Corrosion:  0.007
Eye Irritation:  0.674 Respiratory Toxicity:  0.75
Drug-induced Neurotoxicity:  0.04 Ototoxicity:  0.658
Hematotoxicity:  0.156 Drug-induced Nephrotoxicity:  0.584
Genotoxicity:  0.557 RPMI-8226 Immunitoxicity:  0.044
A549 Cytotoxicity:  0.056 Hek293 Cytotoxicity:  0.27
BCF:   0.998
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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:   4.099
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.604
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.947
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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
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[24195447]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota Gum resin n.a. n.a. PMID[26457560]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15315 Boswellia carterii Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15315 Boswellia carterii Species Burseraceae 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





 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 NPC299488 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
1.0 High Similarity NPC148523
0.7121 Intermediate Similarity NPC86372
0.6714 Remote Similarity NPC26413
0.6515 Remote Similarity NPC602872
0.6087 Remote Similarity NPC471898
0.589 Remote Similarity NPC98874
0.5479 Remote Similarity NPC272075
0.5395 Remote Similarity NPC4036
0.5395 Remote Similarity NPC65120
0.5395 Remote Similarity NPC145067
0.5395 Remote Similarity NPC233455
0.5395 Remote Similarity NPC158030
0.5395 Remote Similarity NPC610635
0.5342 Remote Similarity NPC479748
0.5333 Remote Similarity NPC167193
0.5263 Remote Similarity NPC155120
0.5263 Remote Similarity NPC288833
0.5132 Remote Similarity NPC472806

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC299488 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
0.5395 Remote Similarity NPD7515 Phase 2

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