scPDB - 1dtn entry

Protein Data Bank Entry:

PDB ID : 1dtn

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1996-03-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	15.959
Number of residues:	21
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.777	597.375

% Hydrophobic	% Polar
53.67	46.33
According to VolSite

Ligand :

HET Code:	APG
Formula:	C9H9O3
Molecular weight:	165.166 g/mol
DrugBank ID:	DB07381
Buried Surface Area:	66.09 %
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

X	Y	Z
30.8332	4.77308	17.4987

Binding mode :

What is Poseview ?

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O14	NZ	LYS- 164	3	165.17	H-Bond (Protein Donor)	false
O15	NZ	LYS- 164	3.26	140.02	H-Bond (Protein Donor)	false
O14	NZ	LYS- 164	3	0	Ionic (Protein Cationic)	false
O15	NZ	LYS- 164	3.26	0	Ionic (Protein Cationic)	false
C14	CD	LYS- 166	3.56	0	Hydrophobic	false
O15	NZ	LYS- 166	3.08	0	Ionic (Protein Cationic)	false
C1	CD2	LEU- 298	4.31	0	Hydrophobic	false
C6	CD1	LEU- 298	4.19	0	Hydrophobic	false
O14	NE2	GLN- 317	3.42	138.74	H-Bond (Protein Donor)	false
O15	NE2	GLN- 317	2.86	130.59	H-Bond (Protein Donor)	false
C2	CD1	LEU- 319	4.17	0	Hydrophobic	false
O17	MG	MG- 360	2.48	0	Metal Acceptor	false
O14	MG	MG- 360	2.54	0	Metal Acceptor	false