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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:

1mdr

2.100 Å

X-ray

1993-11-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mandelate racemase
ID:MANR_PSEPU
AC:P11444
Organism:Pseudomonas putida
Reign:Bacteria
TaxID:303
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.037
Number of residues:26
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.599334.125

% Hydrophobic% Polar
54.5545.45
According to VolSite

Ligand :
1mdr_1 Structure
HET Code: APG
Formula: C9H9O3
Molecular weight: 165.166 g/mol
DrugBank ID: DB07381
Buried Surface Area:74.32 %
Polar Surface area: 60.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
30.80764.747517.5957


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
C2CG1VAL- 224.410Hydrophobic
C14CG2THR- 244.420Hydrophobic
C6CG2VAL- 294.390Hydrophobic
O14NZLYS- 1643.680Ionic
(Protein Cationic)
O15NZLYS- 1642.790Ionic
(Protein Cationic)
O15NZLYS- 1642.79161.13H-Bond
(Protein Donor)
C14CDLYS- 1663.530Hydrophobic
O17ND2ASN- 1972.8135.13H-Bond
(Protein Donor)
O17OE2GLU- 2472.75149.44H-Bond
(Ligand Donor)
C1CD2LEU- 2984.050Hydrophobic
O14OE2GLU- 3172.72163.65H-Bond
(Protein Donor)
C2CD1LEU- 3193.780Hydrophobic
O17MG MG- 3602.270Metal Acceptor
O15MG MG- 3602.150Metal Acceptor