Structure

Physi-Chem Properties

Molecular Weight:  240.21
Volume:  274.384
LogP:  3.011
LogD:  3.127
LogS:  -1.398
# Rotatable Bonds:  3
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.744
Synthetic Accessibility Score:  4.252
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.421
MDCK Permeability:  1.5139928109419998e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.121
Plasma Protein Binding (PPB):  83.13282012939453%
Volume Distribution (VD):  0.741
Pgp-substrate:  20.439428329467773%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.295
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.859
CYP2C9-inhibitor:  0.082
CYP2C9-substrate:  0.281
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.105
CYP3A4-inhibitor:  0.237
CYP3A4-substrate:  0.267

ADMET: Excretion

Clearance (CL):  5.148
Half-life (T1/2):  0.34

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.034
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.226
Carcinogencity:  0.046
Eye Corrosion:  0.981
Eye Irritation:  0.973
Respiratory Toxicity:  0.255

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

  Natural Product: NPC41964

Natural Product ID:  NPC41964
Common Name*:   KCUBNAQHLWZMCB-TYNCELHUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KCUBNAQHLWZMCB-TYNCELHUSA-N
Standard InCHI:  InChI=1S/C15H28O2/c1-7-15(6)9-8-11(13(2,3)16)10-12(15)14(4,5)17/h7,11-12,16-17H,1,8-10H2,2-6H3/t11-,12+,15-/m1/s1
SMILES:  C=C[C@]1(C)CC[C@H](C[C@H]1C(C)(C)O)C(C)(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15767775
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002872] Elemane sesquiterpenoids

*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
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19481938]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28294615]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31291099]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1815 Breonia chinensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23384 Rhodiola semenovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21720 Talaromyces variabilis Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10638 Plectranthus myrianthus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7822.1 Eucalyptus globulus subsp. bicostata Subspecies Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3873 Crotalaria candicans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11843 Stephania zippeliana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12091 Martensia denticulata Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12565 Hypericum polyanthemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO526 Salvia sessei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11190 Veronica polita Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5043 Eria japonica Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8934 Gypsophila perfoliata Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11576 Glycosmis macrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9532 Vernonia cistifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10605 Tristania conferta Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22691 Mentha cardiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6289 Ceropegia dichotoma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5456 Juniperus drupacea Species Cupressaceae 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 NPC41964 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 NPC41964 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