Structure

Physi-Chem Properties

Molecular Weight:  288.22
Volume:  311.169
LogP:  2.883
LogD:  2.115
LogS:  -2.414
# Rotatable Bonds:  1
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.743
Synthetic Accessibility Score:  5.151
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.141
MDCK Permeability:  7.093811746017309e-06
Pgp-inhibitor:  0.114
Pgp-substrate:  0.075
Human Intestinal Absorption (HIA):  0.049
20% Bioavailability (F20%):  0.988
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.569
Plasma Protein Binding (PPB):  33.69086837768555%
Volume Distribution (VD):  1.183
Pgp-substrate:  56.66230773925781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.126
CYP1A2-substrate:  0.714
CYP2C19-inhibitor:  0.472
CYP2C19-substrate:  0.931
CYP2C9-inhibitor:  0.438
CYP2C9-substrate:  0.363
CYP2D6-inhibitor:  0.593
CYP2D6-substrate:  0.611
CYP3A4-inhibitor:  0.777
CYP3A4-substrate:  0.84

ADMET: Excretion

Clearance (CL):  6.176
Half-life (T1/2):  0.766

ADMET: Toxicity

hERG Blockers:  0.241
Human Hepatotoxicity (H-HT):  0.605
Drug-inuced Liver Injury (DILI):  0.096
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.274
Maximum Recommended Daily Dose:  0.903
Skin Sensitization:  0.919
Carcinogencity:  0.179
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.927

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

  Natural Product: NPC177008

Natural Product ID:  NPC177008
Common Name*:   RBQBCMDKPKIDLR-MJXUCMMTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RBQBCMDKPKIDLR-MJXUCMMTSA-N
Standard InCHI:  InChI=1S/C18H28N2O/c1-12-9-14-10-17-16(6-4-8-20(17)13(2)21)18(11-12)15(14)5-3-7-19-18/h12,14-15,19H,3-11H2,1-2H3/t12-,14+,15-,18-/m1/s1
SMILES:  C[C@@H]1C[C@H]2CC3=C(CCCN3C(=O)C)[C@@]3(C1)[C@@H]2CCCN3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5462441
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO19825 Litsea japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[14575444]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[16309317]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18499 Podium complanatum Species Sphecidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11060 Doris luteorosea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17577 Azalea ovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19298 Gerbera crocea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17341 Gambeya africana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17887 Penstemon centranthifolius Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19696 Othonna quercifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18023 Vitex quinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21360 Cordia corymbosa Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19869 Fusicolla aquaeductuum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19565 Crocus chrysanthus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18518 Haematomma nemetzii Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae 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 NPC177008 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 NPC177008 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