Structure

Physi-Chem Properties

Molecular Weight:  236.14
Volume:  263.889
LogP:  3.722
LogD:  1.918
LogS:  -3.371
# Rotatable Bonds:  8
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.52
Synthetic Accessibility Score:  2.791
Fsp3:  0.643
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:  -4.759
MDCK Permeability:  5.536813478101976e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.016
Plasma Protein Binding (PPB):  99.2824478149414%
Volume Distribution (VD):  0.414
Pgp-substrate:  1.0819926261901855%

ADMET: Metabolism

CYP1A2-inhibitor:  0.086
CYP1A2-substrate:  0.16
CYP2C19-inhibitor:  0.693
CYP2C19-substrate:  0.413
CYP2C9-inhibitor:  0.839
CYP2C9-substrate:  0.954
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.178
CYP3A4-inhibitor:  0.107
CYP3A4-substrate:  0.039

ADMET: Excretion

Clearance (CL):  3.481
Half-life (T1/2):  0.826

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.191
Drug-inuced Liver Injury (DILI):  0.969
AMES Toxicity:  0.523
Rat Oral Acute Toxicity:  0.145
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.939
Carcinogencity:  0.55
Eye Corrosion:  0.992
Eye Irritation:  0.992
Respiratory Toxicity:  0.902

Download Data

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

  Natural Product: NPC144829

Natural Product ID:  NPC144829
Common Name*:   Monotiporic Acid A
IUPAC Name:   2-dodeca-2,4-diynoxyacetic acid
Synonyms:  
Standard InCHIKey:  FNMQEBVGAFDLDK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H20O3/c1-2-3-4-5-6-7-8-9-10-11-12-17-13-14(15)16/h2-7,12-13H2,1H3,(H,15,16)
SMILES:  CCCCCCCC#CC#CCOCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL445209
PubChem CID:   177348
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001205] Carboxylic acids

*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
NPO15905 Montipora digitata Species Acroporidae Eukaryota eggs n.a. n.a. PMID[8792626]
NPO15905 Montipora digitata Species Acroporidae 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
NPT168 Cell Line P388 Mus musculus IC50 = 5.0 ug.mL-1 PMID[566434]

☑ 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 NPC144829 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
0.9231 High Similarity NPC474205
0.9231 High Similarity NPC225963
0.7755 Intermediate Similarity NPC236872
0.7347 Intermediate Similarity NPC301482
0.7143 Intermediate Similarity NPC473551
0.7083 Intermediate Similarity NPC474204
0.7073 Intermediate Similarity NPC140229
0.6792 Remote Similarity NPC289979
0.6744 Remote Similarity NPC103612
0.6744 Remote Similarity NPC24967
0.6667 Remote Similarity NPC316272
0.6512 Remote Similarity NPC196442
0.6512 Remote Similarity NPC325165
0.6512 Remote Similarity NPC301398
0.6512 Remote Similarity NPC223374
0.6512 Remote Similarity NPC86545
0.65 Remote Similarity NPC232172
0.6471 Remote Similarity NPC26253
0.6279 Remote Similarity NPC286498
0.625 Remote Similarity NPC223195
0.6226 Remote Similarity NPC287811
0.6222 Remote Similarity NPC128996
0.619 Remote Similarity NPC40965
0.6154 Remote Similarity NPC477778
0.6087 Remote Similarity NPC197039
0.6078 Remote Similarity NPC8597
0.6047 Remote Similarity NPC322892
0.6042 Remote Similarity NPC163746
0.6042 Remote Similarity NPC103286
0.6 Remote Similarity NPC80641
0.6 Remote Similarity NPC62014
0.5952 Remote Similarity NPC5934
0.5938 Remote Similarity NPC477980
0.5926 Remote Similarity NPC100096
0.5918 Remote Similarity NPC129972
0.5918 Remote Similarity NPC71317
0.5918 Remote Similarity NPC31121
0.5918 Remote Similarity NPC301528
0.5909 Remote Similarity NPC154396
0.5893 Remote Similarity NPC53463
0.5893 Remote Similarity NPC23155
0.5893 Remote Similarity NPC469937
0.5893 Remote Similarity NPC320588
0.5882 Remote Similarity NPC201948
0.587 Remote Similarity NPC158179
0.5854 Remote Similarity NPC88135
0.5854 Remote Similarity NPC238135
0.5849 Remote Similarity NPC304162
0.5833 Remote Similarity NPC40597
0.5833 Remote Similarity NPC149299
0.5833 Remote Similarity NPC250028
0.5833 Remote Similarity NPC256163
0.5833 Remote Similarity NPC152008
0.5814 Remote Similarity NPC281883
0.5814 Remote Similarity NPC12904
0.58 Remote Similarity NPC255837
0.58 Remote Similarity NPC19305
0.5778 Remote Similarity NPC155872
0.5745 Remote Similarity NPC316546
0.5745 Remote Similarity NPC73245
0.5714 Remote Similarity NPC127696
0.5714 Remote Similarity NPC474361
0.5714 Remote Similarity NPC477781
0.5714 Remote Similarity NPC53541
0.5714 Remote Similarity NPC477780
0.5686 Remote Similarity NPC8219
0.5682 Remote Similarity NPC286695
0.5672 Remote Similarity NPC477983
0.5672 Remote Similarity NPC477981
0.5652 Remote Similarity NPC154642
0.5652 Remote Similarity NPC5505
0.5652 Remote Similarity NPC80396
0.5641 Remote Similarity NPC110107
0.5625 Remote Similarity NPC80234
0.5625 Remote Similarity NPC223249
0.561 Remote Similarity NPC248233
0.56 Remote Similarity NPC203531
0.56 Remote Similarity NPC236579

  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 NPC144829 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
0.5952 Remote Similarity NPD8856 Phase 2
0.5893 Remote Similarity NPD3730 Approved
0.5893 Remote Similarity NPD3728 Approved
0.5833 Remote Similarity NPD7536 Approved
0.5814 Remote Similarity NPD9636 Phase 2

  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