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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1mxf

2.300 Å

X-ray

2002-10-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative pteridine reductase 2
ID:Q8I814_TRYCR
AC:Q8I814
Organism:Trypanosoma cruzi
Reign:Eukaryota
TaxID:5693
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A97 %
D3 %


Ligand binding site composition:

B-Factor:35.003
Number of residues:31
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.550756.000

% Hydrophobic% Polar
52.6847.32
According to VolSite

Ligand :
1mxf_1 Structure
HET Code: MTX
Formula: C20H20N8O5
Molecular weight: 452.423 g/mol
DrugBank ID: DB00563
Buried Surface Area:56.38 %
Polar Surface area: 216.2 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
17.355852.449524.5968


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
NA2OGSER- 1032.7157.05H-Bond
(Ligand Donor)
DuArDuArTYR- 1053.760Aromatic Face/Face
C16CD2LEU- 1763.40Hydrophobic
NA4OHTYR- 1822.82165.26H-Bond
(Ligand Donor)
CMCD1LEU- 2143.510Hydrophobic
C9CD2LEU- 2174.420Hydrophobic
C13CGPRO- 2183.880Hydrophobic
C12CEMET- 2213.870Hydrophobic
CGCEMET- 2214.060Hydrophobic
OOHTYR- 2292.99147.75H-Bond
(Protein Donor)
CGCZTYR- 2294.280Hydrophobic
N1O2ANDP- 12772.89151.3H-Bond
(Ligand Donor)
NA2O2ANDP- 12773.11140.71H-Bond
(Ligand Donor)