Structure

Physi-Chem Properties

Molecular Weight:  428.37
Volume:  482.302
LogP:  6.732
LogD:  5.066
LogS:  -5.784
# Rotatable Bonds:  0
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.419
Synthetic Accessibility Score:  4.908
Fsp3:  0.931
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.751
MDCK Permeability:  1.3401558135228697e-05
Pgp-inhibitor:  0.816
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.99
30% Bioavailability (F30%):  0.925

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.257
Plasma Protein Binding (PPB):  89.76093292236328%
Volume Distribution (VD):  1.086
Pgp-substrate:  8.298993110656738%

ADMET: Metabolism

CYP1A2-inhibitor:  0.033
CYP1A2-substrate:  0.146
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.874
CYP2C9-inhibitor:  0.157
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.089
CYP3A4-inhibitor:  0.547
CYP3A4-substrate:  0.351

ADMET: Excretion

Clearance (CL):  13.314
Half-life (T1/2):  0.091

ADMET: Toxicity

hERG Blockers:  0.57
Human Hepatotoxicity (H-HT):  0.282
Drug-inuced Liver Injury (DILI):  0.014
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.282
Maximum Recommended Daily Dose:  0.979
Skin Sensitization:  0.953
Carcinogencity:  0.24
Eye Corrosion:  0.149
Eye Irritation:  0.05
Respiratory Toxicity:  0.894

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC2114

Natural Product ID:  NPC2114
Common Name*:   LCDBRGPJMWXDGF-ZIAGYGMSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LCDBRGPJMWXDGF-ZIAGYGMSSA-N
Standard InCHI:  InChI=1S/C16H27NO3/c1-3-4-5-6-7-10-15(19)13(2)16(20)17-11-8-9-14(17)12-18/h3-4,13-14,18H,5-12H2,1-2H3/t13-,14-/m1/s1
SMILES:  CC=CCCCCC(=O)[C@@H](C)C(=O)N1CCC[C@@H]1CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0003023] N-acylpyrrolidines

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. twig n.a. DOI[10.1021/np50063a031]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. stem n.a. DOI[10.1021/np50063a031]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. PMID[11277746]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[15165134]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. twig n.a. PMID[16254827]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. stem n.a. PMID[16254827]
NPO16566 Cinnamosma madagascariensis Species Canellaceae Eukaryota n.a. n.a. n.a. PMID[18179176]
NPO17999 Sonneratia alba Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[19835393]
NPO22097 Plakinastrella clathrata Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[21261297]
NPO16812 Ajuga bracteosa Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[21539300]
NPO9189 Streptomyces atratus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21868221]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[22316191]
NPO5119 Pseudomonas chlororaphis Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25679537]
NPO5119 Pseudomonas chlororaphis Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25901993]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[2778454]
NPO15599 Daldinia concentrica Species n.a. Eukaryota Fruiting Bodies n.a. n.a. PMID[29715021]
NPO16455 Xylopia aethiopica Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[8158166]
NPO14575 Periploca forrestii Species Cosmopterigidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15004 Artemisia taurica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26788 Sophora viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11760 Teucrium orientale Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8010 Otostegia fruticosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15004 Artemisia taurica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26788 Sophora viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14575 Periploca forrestii Species Cosmopterigidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4507 Bruguiera gymnorhiza Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21437 Rhododendron aureum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15004 Artemisia taurica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15599 Daldinia concentrica Species n.a. Eukaryota n.a. n.a. n.a. Database[Title]
NPO28821 Stichopus horrens Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17844 Agaricus integer Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17602 Arbutus menziesii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13013 Saccharothrix mutabilis Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16695 Fumaria kraliki Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4507 Bruguiera gymnorhiza Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7905 Lepista irina Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8010 Otostegia fruticosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16329 Potebniamyces gallicola Species Phacidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9951 Hyella caespitosa Species Hyellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11760 Teucrium orientale Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18073 Justicia trinervia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2550 Trichoderma citrinum Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15545 Veltheimia viridifolia Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO84 Isoberlinia angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15004 Artemisia taurica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9189 Streptomyces atratus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13789 Paranephelius uniflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14575 Periploca forrestii Species Cosmopterigidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22097 Plakinastrella clathrata Species Plakinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17304 Sipunculus nudus Species Sipunculidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10770 Ptilota pectinata Species Ceramiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14002 Petalostemon purpureum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11408 Podocarpus amarus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17921 Allium monspessulanum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17145 Aegiceras corniculatum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16215 Umbilicaria cinereorufescens Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26788 Sophora viciifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15919 Streptomyces caelestis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21437 Rhododendron aureum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16923 Cereus chrysacanthus Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17071 Coeloseira pacifica Species Champiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17999 Sonneratia alba Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16566 Cinnamosma madagascariensis Species Canellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17375 Ceramium botryocarpum Species Ceramiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28319 Ulva prolifera Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16456 Mirabilis jalapa Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16455 Xylopia aethiopica Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17339 Macaranga sinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28868 Pardachirus pavoninus Species Soleidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17218 Helichrysum nudifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4336 Echiochilon pauciflorum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5119 Pseudomonas chlororaphis Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25550 Buchenavia tetraphylla Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16052 Chromodoris obsoleta Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15599 Daldinia concentrica Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2155 Tephroseris integrifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14813 Agaricus silvaticus Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15748 Hypoxis nyasica Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16812 Ajuga bracteosa Species Lamiaceae 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC2114 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC2114 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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