Natural Product: NPC180020

Natural Product IDNPC180020
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LWHOLPPVYKATGS-YUPDMNDNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132488068
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane diterpenoids

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 LWHOLPPVYKATGS-YUPDMNDNSA-N
Standard InCHI InChI=1S/C20H32O2/c1-12-13-5-6-16-19(4)11-14(21)10-18(2,3)15(19)7-8-20(16,9-13)17(12)22/h13-17,21-22H,1,5-11H2,2-4H3/t13-,14-,15-,16+,17+,19-,20-/m1/s1
SMILES C=C1[C@@H]2CC[C@H]3[C@]4(C)C[C@@H](CC(C)(C)[C@H]4CC[C@]3(C2)[C@H]1O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   304.24 Volume:   335.194
?
Van der Waals volume.
Dense:   0.908 LogP:   2.897
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.111
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.704
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   20.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.666 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.767 Fsp3:   0.9
MCE-18:   102.316
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.418 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.016
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.73 Promiscuous compounds:   0.085

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.598 MDCK Permeability:   -4.688
Pgp-inhibitor:   0.068 Pgp-substrate:   0.103
PAMPA:   0.447
?
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):   0.002
20% Bioavailability (F20%):   0.261 30% Bioavailability (F30%):   0.164
50% Bioavailability (F50%):   0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.682 MRP1:   0.135
Plasma Protein Binding (PPB):   80.561% Volume Distribution (VD):   -0.05
Fu: 19.566%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.986 BCRP inhibitor:   0.889
BSEP inhibitor:   0.865

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.003
CYP2C19-inhibitor:   0.137 CYP2C19-substrate:   0.049
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.288
CYP2D6-inhibitor:   0.101 CYP2D6-substrate:   0.417
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.968
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.296
HLM stability:   0.955
?
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):  9.714 Half-life (T1/2):  1.694

ADMET: Toxicity

hERG Blockers:  0.126 hERG Blockers (10um):  0.323
Human Hepatotoxicity (H-HT):  0.505 Drug-induced Liver Injury (DILI):  0.274
AMES Toxicity:  0.673 Rat Oral Acute Toxicity:  0.493
Maximum Recommended Daily Dose:  0.729 Skin Sensitization:  0.972
Carcinogencity:  0.656 Eye Corrosion:  0.078
Eye Irritation:  0.782 Respiratory Toxicity:  0.819
Drug-induced Neurotoxicity:  0.493 Ototoxicity:  0.557
Hematotoxicity:  0.342 Drug-induced Nephrotoxicity:  0.72
Genotoxicity:  0.303 RPMI-8226 Immunitoxicity:  0.101
A549 Cytotoxicity:  0.668 Hek293 Cytotoxicity:  0.559
BCF:   1.897
?
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:   3.942
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.375
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.77
?
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
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[11087590]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota Whole plant n.a. n.a. PMID[18181575]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota fruits n.a. n.a. PMID[19902967]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. stem n.a. PMID[23157017]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[23157017]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. Chinese liverworts n.a. PMID[24491225]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. PMID[28006909]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Europe PMC[305622]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[37447036]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[38794396]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO14630 Boronia ramosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7868 Xeromphis obovata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1890 Lidbeckia pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12294 Kydia calycina Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13236 Viguiera multiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8611 Cornutia grandifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15726 Rudbeckia subtomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9155 Kageneckia angustifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13360 Passiflora racemosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2312 Encephalosphaera lasiandra Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15306 Smilax japonica Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15818 Lycianthes marlipoensis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1890 Lidbeckia pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12517 Tylophora cordifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7056 Pedinophyllum interruptum Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7868 Xeromphis obovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8866 Papaver atlanticum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11567 Picradeniopsis absinthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12294 Kydia calycina Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10624 Solidago wrightii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14630 Boronia ramosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27787 Pseudocentrotus depressus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13236 Viguiera multiflora Species Asteraceae 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
NPT2615 Cell line HEK-293T Homo sapiens Activity = 100.0 % PMID[28006909]

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 NPC180020 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
0.7805 Intermediate Similarity NPC38141
0.7143 Intermediate Similarity NPC164045
0.7143 Intermediate Similarity NPC312989
0.6364 Remote Similarity NPC472506
0.6087 Remote Similarity NPC152728
0.5957 Remote Similarity NPC138502
0.587 Remote Similarity NPC472500
0.587 Remote Similarity NPC472499
0.56 Remote Similarity NPC46881
0.5385 Remote Similarity NPC263974
0.5306 Remote Similarity NPC475
0.5306 Remote Similarity NPC472502
0.5192 Remote Similarity NPC170985

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC180020 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