Structure

Physi-Chem Properties

Molecular Weight:  266.12
Volume:  272.913
LogP:  2.378
LogD:  1.612
LogS:  -2.839
# Rotatable Bonds:  5
TPSA:  72.83
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.672
Synthetic Accessibility Score:  2.627
Fsp3:  0.429
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:  -4.733
MDCK Permeability:  2.5223474949598312e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.697
20% Bioavailability (F20%):  0.819
30% Bioavailability (F30%):  0.128

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.932
Plasma Protein Binding (PPB):  80.97509002685547%
Volume Distribution (VD):  0.507
Pgp-substrate:  40.12938690185547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.832
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.198
CYP2C19-substrate:  0.465
CYP2C9-inhibitor:  0.517
CYP2C9-substrate:  0.792
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.252
CYP3A4-inhibitor:  0.136
CYP3A4-substrate:  0.305

ADMET: Excretion

Clearance (CL):  1.329
Half-life (T1/2):  0.783

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.002
Drug-inuced Liver Injury (DILI):  0.183
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.853
Maximum Recommended Daily Dose:  0.086
Skin Sensitization:  0.844
Carcinogencity:  0.108
Eye Corrosion:  0.159
Eye Irritation:  0.898
Respiratory Toxicity:  0.482

Download Data

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

  Natural Product: NPC225105

Natural Product ID:  NPC225105
Common Name*:   FIDBMXMVNZTDHE-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FIDBMXMVNZTDHE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H18O5/c1-7(2)12-11(18-9(4)15)6-8(3)13(17)14(12)19-10(5)16/h6-7,17H,1-5H3
SMILES:  CC(C)c1c(cc(C)c(c1OC(=O)C)O)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0000051] Aromatic monoterpenoids

*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
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[10869193]
NPO27360 Pyracantha fortuneana Species Rosaceae Eukaryota fruit n.a. n.a. PMID[16872137]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Berries n.a. n.a. PMID[18314960]
NPO11654 Eusynstyela misakiensis Species n.a. n.a. n.a. n.a. n.a. PMID[19505081]
NPO15436 Brucea mollis Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[22070654]
NPO15436 Brucea mollis Species Simaroubaceae Eukaryota stems n.a. n.a. PMID[22070654]
NPO15436 Brucea mollis Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[24199564]
NPO11654 Eusynstyela misakiensis Species n.a. n.a. n.a. n.a. n.a. PMID[7931370]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13652 Laurilia sulcata Species Corticiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14275 Carissa opaca Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15152 Fagara leprieurii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14854 Stereocaulon ramulosum Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15618 Teucrium luteum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12504 Penstemon acuminatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6262 Rumphella aggregata Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3209 Anchusa strigosa Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15532 Polygala crotalarioides Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11654 Eusynstyela misakiensis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15243 Pimenta dioica Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27360 Pyracantha fortuneana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3904 Casearia esculenta Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15436 Brucea mollis Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1685 Mespilodaphne pretiosa n.a. n.a. n.a. 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 NPC225105 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 NPC225105 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