scPDB - 1mdl entry

Protein Data Bank Entry:

PDB ID : 1mdl

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 1996-03-29

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:	15.619
Number of residues:	17
Including
Standard Amino Acids:	16
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.198	550.125

% Hydrophobic	% Polar
49.08	50.92
According to VolSite

Ligand :

HET Code:	RMN
Formula:	C8H7O3
Molecular weight:	151.139 g/mol
DrugBank ID:	DB02280
Buried Surface Area:	48.9 %
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
36.4575	2.06936	18.0316

Binding mode :

What is Poseview ?

2D View
3D View

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
C4	CD1	LEU- 18	3.73	0	Hydrophobic	false
C5	CG1	VAL- 22	3.8	0	Hydrophobic	false
C3	CG2	VAL- 29	3.63	0	Hydrophobic	false
C4	CB	ALA- 32	4.42	0	Hydrophobic	false
O11	CZ	ARG- 166	3.04	0	Ionic (Protein Cationic)	false
O12	CZ	ARG- 166	3.59	0	Ionic (Protein Cationic)	false
O12	NH1	ARG- 166	2.91	142.67	H-Bond (Protein Donor)	false
C5	CD2	LEU- 321	4.41	0	Hydrophobic	false