Structure

Physi-Chem Properties

Molecular Weight:  290.26
Volume:  340.881
LogP:  5.321
LogD:  4.383
LogS:  -5.602
# Rotatable Bonds:  4
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.678
Synthetic Accessibility Score:  4.258
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.522
MDCK Permeability:  1.4340876077767462e-05
Pgp-inhibitor:  0.872
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.805
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.311
Plasma Protein Binding (PPB):  86.9149398803711%
Volume Distribution (VD):  1.184
Pgp-substrate:  12.627254486083984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.133
CYP1A2-substrate:  0.252
CYP2C19-inhibitor:  0.238
CYP2C19-substrate:  0.874
CYP2C9-inhibitor:  0.388
CYP2C9-substrate:  0.35
CYP2D6-inhibitor:  0.109
CYP2D6-substrate:  0.549
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  4.856
Half-life (T1/2):  0.074

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.105
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.441
Maximum Recommended Daily Dose:  0.623
Skin Sensitization:  0.244
Carcinogencity:  0.517
Eye Corrosion:  0.9
Eye Irritation:  0.868
Respiratory Toxicity:  0.948

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Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC67840

Natural Product ID:  NPC67840
Common Name*:   CECREIRZLPLYDM-QGZVKYPTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CECREIRZLPLYDM-QGZVKYPTSA-N
Standard InCHI:  InChI=1S/C20H34O/c1-7-19(5,21)14-11-16-15(2)9-10-17-18(3,4)12-8-13-20(16,17)6/h7,16-17,21H,1-2,8-14H2,3-6H3/t16-,17-,19-,20+/m0/s1
SMILES:  C=C[C@@](C)(CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3034394
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO21179 Streptomyces griseoaurantiacus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[10048567]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[29303577]
NPO26657 Conocephalum conicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. PMID[33264011]
NPO26657 Conocephalum conicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18881 Loropetalum chinense Species Hamamelidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26657 Conocephalum conicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14307 Rhizopus oryzae Species Rhizopodaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18881 Loropetalum chinense Species Hamamelidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26657 Conocephalum conicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26657 Conocephalum conicum Species Conocephalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18881 Loropetalum chinense Species Hamamelidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20425 Epimedium macranthum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23194 Berberis beaniana Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21704 Papaver suaveolens Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23157 Wigandia kunthii Species Namaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18881 Loropetalum chinense Species Hamamelidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14307 Rhizopus oryzae Species Rhizopodaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22147 Goniothalamus macrophyllus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21894 Psychotria granadensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13308 Polycitor adriaticus Species Polycitoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22968 Elaeocarpus serratus Species Elaeocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21179 Streptomyces griseoaurantiacus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15469 Myodocarpus gracilis Species Myodocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22530 Vigna luteola Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6953.1 Aconitum sachalinense subsp. yezoense Subspecies Ranunculaceae 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
NPT22036 CELL-LINE HL Homo sapiens Activity = 88.6 % PMID[456477]
NPT5310 Organism Chlamydophila pneumoniae Chlamydophila pneumoniae Inhibition = 60.0 % PMID[456477]
NPT5310 Organism Chlamydophila pneumoniae Chlamydophila pneumoniae IC50 = 35500.0 nM PMID[456477]

☑ 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 NPC67840 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 NPC67840 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