Structure

Physi-Chem Properties

Molecular Weight:  434.27
Volume:  451.562
LogP:  4.808
LogD:  3.76
LogS:  -4.692
# Rotatable Bonds:  6
TPSA:  78.9
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.483
Synthetic Accessibility Score:  4.628
Fsp3:  0.88
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.854
MDCK Permeability:  6.360127736115828e-05
Pgp-inhibitor:  0.995
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.036
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.195
Plasma Protein Binding (PPB):  60.96458435058594%
Volume Distribution (VD):  1.598
Pgp-substrate:  21.853334426879883%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.046
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.554
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.039
CYP2D6-inhibitor:  0.214
CYP2D6-substrate:  0.084
CYP3A4-inhibitor:  0.556
CYP3A4-substrate:  0.435

ADMET: Excretion

Clearance (CL):  2.858
Half-life (T1/2):  0.305

ADMET: Toxicity

hERG Blockers:  0.14
Human Hepatotoxicity (H-HT):  0.3
Drug-inuced Liver Injury (DILI):  0.933
AMES Toxicity:  0.233
Rat Oral Acute Toxicity:  0.047
Maximum Recommended Daily Dose:  0.926
Skin Sensitization:  0.968
Carcinogencity:  0.389
Eye Corrosion:  0.379
Eye Irritation:  0.101
Respiratory Toxicity:  0.922

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

  Natural Product: NPC312312

Natural Product ID:  NPC312312
Common Name*:   MFAZHXZFFOFQJM-DPPNWCLYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MFAZHXZFFOFQJM-DPPNWCLYSA-N
Standard InCHI:  InChI=1S/C12H18O5/c1-8(10(13)7-11(14)15)5-3-4-6-9(2)12(16)17/h3-4,6,8,10,13H,5,7H2,1-2H3,(H,14,15)(H,16,17)/b4-3+,9-6+/t8-,10-/m1/s1
SMILES:  C[C@H](C/C=C/C=C(C)/C(=O)O)[C@@H](CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000299] Medium-chain hydroxy acids and derivatives

*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
NPO4181 Pseudoalteromonas luteoviolacea Species Pseudoalteromonadaceae Bacteria n.a. n.a. n.a. PMID[20973551]
NPO19301 Blatta orientalis Species Blattoidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19301 Blatta orientalis Species Blattoidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23241 Sigesbeckia orientalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23241 Sigesbeckia orientalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20038 Acritopappus prunifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21795 Aplysia californica Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23212 Vernonia diffusa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21500 Aconitum mokchangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22936 Myrtillocactus geometrizan Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22502 Paraixeris pinnatipartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23054 Senecio atratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4181 Pseudoalteromonas luteoviolacea Species Pseudoalteromonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21734 Scutellaria woronowii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19301 Blatta orientalis Species Blattoidae 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 NPC312312 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 NPC312312 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