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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:

1rx2

1.800 Å

X-ray

1996-09-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydrofolate reductase
ID:DYR_ECOLI
AC:P0ABQ4
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:1.5.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.067
Number of residues:35
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.290334.125

% Hydrophobic% Polar
70.7129.29
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1rx2HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80255075Highcharts.com
Ligand :
1rx2_1 Structure
HET Code: FOL
Formula: C19H17N7O6
Molecular weight: 439.382 g/mol
DrugBank ID: DB00158
Buried Surface Area:57.73 %
Polar Surface area: 214.64 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
33.095742.34247.70041
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1rx2RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


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
C13CEMET- 204.060Hydrophobic
NA2OD1ASP- 272.97169.34H-Bond
(Ligand Donor)
N3OD2ASP- 272.62168.65H-Bond
(Ligand Donor)
CBCBLEU- 284.390Hydrophobic
C11CD2LEU- 284.260Hydrophobic
C16CE2PHE- 313.430Hydrophobic
CBCBLYS- 324.210Hydrophobic
C9CG2THR- 464.10Hydrophobic
C9CD1ILE- 504.090Hydrophobic
C15CD1ILE- 5040Hydrophobic
C14CG1ILE- 503.880Hydrophobic
C16CD2LEU- 544.230Hydrophobic
O1CZARG- 573.480Ionic
(Protein Cationic)
O2CZARG- 573.510Ionic
(Protein Cationic)
O1NH2ARG- 573.39128.44H-Bond
(Protein Donor)
O1NH1ARG- 572.7163.35H-Bond
(Protein Donor)
O2NH2ARG- 572.63174.16H-Bond
(Protein Donor)
C9C4NNAP- 1643.670Hydrophobic
NA2OHOH- 3022.93140.63H-Bond
(Ligand Donor)
O4OHOH- 3622.82179.96H-Bond
(Protein Donor)