Structure

Physi-Chem Properties

Molecular Weight:  213.99
Volume:  135.157
LogP:  1.765
LogD:  1.301
LogS:  -2.705
# Rotatable Bonds:  3
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.712
Synthetic Accessibility Score:  2.542
Fsp3:  0.75
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:  -5.263
MDCK Permeability:  1.567094113852363e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.431
Plasma Protein Binding (PPB):  86.5266342163086%
Volume Distribution (VD):  0.529
Pgp-substrate:  7.71880578994751%

ADMET: Metabolism

CYP1A2-inhibitor:  0.072
CYP1A2-substrate:  0.835
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.838
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.103
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.092
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.338

ADMET: Excretion

Clearance (CL):  1.51
Half-life (T1/2):  0.866

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.226
Drug-inuced Liver Injury (DILI):  0.301
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.399
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.736
Carcinogencity:  0.615
Eye Corrosion:  0.998
Eye Irritation:  0.932
Respiratory Toxicity:  0.95

Download Data

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

  Natural Product: NPC259649

Natural Product ID:  NPC259649
Common Name*:   2,2,3,3,4,4,4-Heptafluorobutanoic Acid
IUPAC Name:   2,2,3,3,4,4,4-heptafluorobutanoic acid
Synonyms:   2,2,3,3,4,4,4-Heptafluoro-Butyric Acid
Standard InCHIKey:  YPJUNDFVDDCYIH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4HF7O2/c5-2(6,1(12)13)3(7,8)4(9,10)11/h(H,12,13)
SMILES:  OC(=O)C(C(C(F)(F)F)(F)F)(F)F
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL367680
PubChem CID:   9777
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000267] Organohalogen compounds
      • [CHEMONTID:0002867] Alkyl halides
        • [CHEMONTID:0001027] Alkyl fluorides
          • [CHEMONTID:0003962] Perfluoroalkyl carboxylic acid 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
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26650 Terminalia chebula Species Combretaceae 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
NPT32 Organism Mus musculus Mus musculus Activity = 101.0 % PMID[528711]

☑ 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 NPC259649 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
0.6857 Remote Similarity NPC326532
0.6552 Remote Similarity NPC149209
0.6129 Remote Similarity NPC236709
0.5938 Remote Similarity NPC122768
0.5938 Remote Similarity NPC151140
0.5938 Remote Similarity NPC292641
0.5938 Remote Similarity NPC174368
0.5938 Remote Similarity NPC104195
0.5938 Remote Similarity NPC61066
0.5769 Remote Similarity NPC7922
0.5758 Remote Similarity NPC320981
0.5758 Remote Similarity NPC198126
0.5714 Remote Similarity NPC181153

  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 NPC259649 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
0.6857 Remote Similarity NPD9513 Phase 1
0.6129 Remote Similarity NPD8594 Approved
0.6129 Remote Similarity NPD8593 Approved
0.5938 Remote Similarity NPD8619 Approved
0.5938 Remote Similarity NPD8617 Approved
0.5758 Remote Similarity NPD8590 Approved
0.5758 Remote Similarity NPD8618 Approved
0.5714 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8615 Phase 2
0.5714 Remote Similarity NPD8201 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