Structure

Physi-Chem Properties

Molecular Weight:  235.13
Volume:  262.57
LogP:  2.458
LogD:  1.425
LogS:  -2.088
# Rotatable Bonds:  8
TPSA:  49.36
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.468
Synthetic Accessibility Score:  3.345
Fsp3:  0.643
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:  -4.161
MDCK Permeability:  7.114044274203479e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  99.07366943359375%
Volume Distribution (VD):  0.535
Pgp-substrate:  1.0494437217712402%

ADMET: Metabolism

CYP1A2-inhibitor:  0.268
CYP1A2-substrate:  0.126
CYP2C19-inhibitor:  0.537
CYP2C19-substrate:  0.436
CYP2C9-inhibitor:  0.797
CYP2C9-substrate:  0.431
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.088
CYP3A4-inhibitor:  0.135
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  2.753
Half-life (T1/2):  0.801

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.91
Drug-inuced Liver Injury (DILI):  0.961
AMES Toxicity:  0.837
Rat Oral Acute Toxicity:  0.137
Maximum Recommended Daily Dose:  0.06
Skin Sensitization:  0.953
Carcinogencity:  0.642
Eye Corrosion:  0.994
Eye Irritation:  0.992
Respiratory Toxicity:  0.888

Download Data

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

  Natural Product: NPC474205

Natural Product ID:  NPC474205
Common Name*:   Montiporic Acid A Sodium Salt
IUPAC Name:   sodium;2-dodeca-2,4-diynoxyacetate
Synonyms:   Montiporic Acid A Sodium Salt
Standard InCHIKey:  PKBDELBTWHEDCZ-UHFFFAOYSA-M
Standard InCHI:  InChI=1S/C14H20O3.Na/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);/q;+1/p-1
SMILES:  CCCCCCCC#CC#CCOCC(=O)[O-].[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463467
PubChem CID:   44567166
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001166] Carboxylic acid salts

*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
NPO33414 montipora sp. Species Acroporidae Eukaryota n.a. n.a. n.a. PMID[11087594]
NPO33414 montipora sp. Species Acroporidae Eukaryota n.a. n.a. n.a. PMID[11520227]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 = 6.31 ug ml-1 PMID[452453]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 7.5 ug ml-1 PMID[452453]
NPT574 Cell Line XF498 Homo sapiens ED50 = 7.72 ug ml-1 PMID[452453]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 7.97 ug ml-1 PMID[452453]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 8.3 ug ml-1 PMID[452453]

☑ 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 NPC474205 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
1.0 High Similarity NPC225963
0.9231 High Similarity NPC144829
0.7826 Intermediate Similarity NPC301482
0.7632 Intermediate Similarity NPC140229
0.7609 Intermediate Similarity NPC473551
0.7556 Intermediate Similarity NPC474204
0.7143 Intermediate Similarity NPC236872
0.7027 Intermediate Similarity NPC232172
0.7 Intermediate Similarity NPC196442
0.7 Intermediate Similarity NPC86545
0.7 Intermediate Similarity NPC301398
0.7 Intermediate Similarity NPC223374
0.675 Remote Similarity NPC286498
0.6667 Remote Similarity NPC40965
0.6667 Remote Similarity NPC128996
0.66 Remote Similarity NPC287811
0.65 Remote Similarity NPC322892
0.6429 Remote Similarity NPC80641
0.641 Remote Similarity NPC5934
0.6341 Remote Similarity NPC154396
0.6316 Remote Similarity NPC88135
0.625 Remote Similarity NPC281883
0.625 Remote Similarity NPC12904
0.6226 Remote Similarity NPC289979
0.6222 Remote Similarity NPC40597
0.6222 Remote Similarity NPC256163
0.6222 Remote Similarity NPC250028
0.6222 Remote Similarity NPC149299
0.619 Remote Similarity NPC155872
0.6154 Remote Similarity NPC127696
0.6136 Remote Similarity NPC316546
0.6111 Remote Similarity NPC110107
0.6098 Remote Similarity NPC286695
0.6087 Remote Similarity NPC53541
0.6053 Remote Similarity NPC248233
0.6047 Remote Similarity NPC80396
0.6047 Remote Similarity NPC154642
0.6047 Remote Similarity NPC24967
0.6047 Remote Similarity NPC103612
0.6 Remote Similarity NPC223249
0.6 Remote Similarity NPC80234
0.5957 Remote Similarity NPC203531
0.5957 Remote Similarity NPC236579
0.5946 Remote Similarity NPC3693
0.5946 Remote Similarity NPC41485
0.5946 Remote Similarity NPC32280
0.5909 Remote Similarity NPC14608
0.5897 Remote Similarity NPC223195
0.5897 Remote Similarity NPC316272
0.5882 Remote Similarity NPC26253
0.587 Remote Similarity NPC165533
0.5833 Remote Similarity NPC23508
0.5814 Remote Similarity NPC325165
0.5789 Remote Similarity NPC201132
0.5789 Remote Similarity NPC166804
0.5789 Remote Similarity NPC127134
0.5778 Remote Similarity NPC201622
0.5778 Remote Similarity NPC305660
0.5778 Remote Similarity NPC54980
0.5778 Remote Similarity NPC22903
0.5769 Remote Similarity NPC55678
0.5745 Remote Similarity NPC163746
0.5745 Remote Similarity NPC103286
0.5714 Remote Similarity NPC147054
0.5714 Remote Similarity NPC287231
0.5714 Remote Similarity NPC35371
0.5714 Remote Similarity NPC47363
0.5714 Remote Similarity NPC168714
0.5714 Remote Similarity NPC41007
0.5714 Remote Similarity NPC178643
0.5652 Remote Similarity NPC31551
0.5652 Remote Similarity NPC81263
0.5652 Remote Similarity NPC219536
0.5645 Remote Similarity NPC477982
0.5641 Remote Similarity NPC143211
0.5636 Remote Similarity NPC269615
0.5625 Remote Similarity NPC71317
0.5625 Remote Similarity NPC129972
0.5625 Remote Similarity NPC301528
0.56 Remote Similarity NPC52700
0.56 Remote Similarity NPC63182
0.56 Remote Similarity NPC145045
0.56 Remote Similarity NPC105329

  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 NPC474205 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
0.641 Remote Similarity NPD8856 Phase 2
0.625 Remote Similarity NPD9636 Phase 2
0.5789 Remote Similarity NPD8989 Approved
0.575 Remote Similarity NPD9191 Approved
0.5714 Remote Similarity NPD2699 Approved
0.5686 Remote Similarity NPD6125 Clinical (unspecified phase)

  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