Examples: STIGLCNAGHEMCLC_000191PRD_000468

MTX

Drug-like

METHOTREXATE

Description

Synonyms
MTX, Folex, Zexate, Trexan, Mexate, Maxtrex, Ebetrex, Atrexe...Show more
Formula
C20 H22 N8 O5
Standard InChI
InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/...Show more
Standard InChI Key
FBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C...Show more
Source OpenEye
Is part of
First observed in

Overall view, and highlighted
scaffolds and fragments 

This image gallery displays several views of the ligand structure:

  • Basic Structural Representation: Shows the overall structure of the ligand.
  • Detailed Structural Representation: Highlights individual atoms within the ligand.
  • Murcko Scaffold: Presents the scaffold of the ligand highlighted in yellow.
  • Highlighted Fragments: Displays various ligand fragments, highlighted in yellow.

Displayed: 1 / 2

Physicochemical properties

Molecular properties
Molecular weight
Total mass of the molecule in Daltons
454.2 Da
Labute accessible surface area
Accessible surface area according to the Labute's definition
218.4 Å 2
Heavy atoms
Number of non-hydrogen atoms
33
Heteroatoms
Number of non-oxygen and non-carbon atoms
13
Carbon SP3 value
Fraction of C atoms that are SP3 hybridized
0.3
Wildman-Crippen molar refractivity
Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability
113.1
Wildman-Crippen Log P
Octanol/Water partition coefficient predicted using Wildman-Crippen method
-1.4
Conformational properties
Rotatable bonds
Number of single bonds, not part of a ring bound to a nonterminal heavy atom
12
Ring properties
Aromatic rings
Number of aromatic rings
3
Rings
Number of rings
3
Aliphatic rings
Number of aliphatic rings
0
Heterocycles
Number or rings with at least two different elements
2
Saturated rings
Number of saturated rings
0
Aromatic heterocycles
Number of aromatic heterocyles
2
Saturated heterocycles
Number of saturated heterocyles
0
Aliphatic heterocycles
Number of aliphatic heterocycles
0
Spiro atoms
Atoms shared between rings that share exactly one atom
0
Bridgehead atoms
Number of atoms shared between rings that share at least two bonds
0
Surface properties
Topological surface area
Topological surface area
210.5
Functional group properties
Hydrogen bond donors
Number of hydrogen bond donors
5
Hydrogen bond acceptors
Number of hydrogen bond acceptors
12
Amide bonds
Number of amide bonds
1
Stereochemical properties
Stereocenters
Number of atoms with four attachments different from each other
1

Bound structures

Found as a bound ligand in 36 distinct proteins and 83 PDB Structures. Group data by:

Protein name

Reduced folate transporter

PDB-KB Proteins

P41440

EC number

---

Ligand annotation

Drug-like

Total structures

1

Protein name

Bifunctional dihydrofolate reductase-thymidylate synthase

PDB-KB Proteins

P13922

EC number

1.5.1.3, 2.1.1.45

Ligand annotation

Unannotated

Total structures

2

Protein name

Bifunctional dihydrofolate reductase-thymidylate synthase

PDB-KB Proteins

A0A0S4TER9

EC number

1.5.1.3, 2.1.1.45

Ligand annotation

Unannotated

Total structures

27

Protein name

ATP-binding cassette sub-family C member 4

PDB-KB Proteins

O15439

EC number

7.6.2.-, 7.6.2.3, 7.6.2.2

Ligand annotation

Unannotated

Total structures

2

Protein name

Bifunctional protein FolD

PDB-KB Proteins

Q0PA35

EC number

3.5.4.9, 1.5.1.5

Ligand annotation

Unannotated

Total structures

1

Items per page:
1 – 5 of 37

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of MTX from 150 ligand instances in 36 distinct proteins and 83 PDB Structures. The protein-ligand interactions are computed using PDBe Arpeggio
Documentation

Ligand atoms

Sort by:
Ligand interactions

Percentage of interactions by ligand atom compared to the total interactions of the ligand

Amino acid interactions

Percentage of interactions between ligand atom-amino acid pair compared to the total interactions of the amino acid

Icons:
Positively charged
Negatively charged
Polar
Hydrophobic
Aromatic
Aromatic (Trp)
Glycine
Cysteine
Proline

Atom-wise interactions of MTX molecule

Percentage of interactions by ligand atom compared to the total interactions of the ligand

For full interaction statistics, including the heatmap showing ligand atom interaction frequency with different amino acids, please view on a larger screen