scPDB - 4lut entry

Protein Data Bank Entry:

PDB ID : 4lut

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2013-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alanine racemase
ID:	Q180W0_PEPD6
AC:	Q180W0
Organism:	Peptoclostridium difficile
Reign:	Bacteria
TaxID:	272563
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	78 %
B	22 %

Ligand binding site composition:

B-Factor:	25.488
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.983	1370.250

% Hydrophobic	% Polar
32.51	67.49
According to VolSite

Ligand :

HET Code:	DCS
Formula:	C11H15N3O7P
Molecular weight:	332.226 g/mol
DrugBank ID:	DB02038
Buried Surface Area:	69.22 %
Polar Surface area:	170.29 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
26.1541	46.5393	95.9959

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
C5A	CG2	VAL- 37	4	0	Hydrophobic	false
O2P	OH	TYR- 43	2.58	155.09	H-Bond (Protein Donor)	false
C2A	CD2	LEU- 85	3.75	0	Hydrophobic	false
C3	CD1	LEU- 85	4.15	0	Hydrophobic	false
C2A	CE2	PHE- 165	4.37	0	Hydrophobic	false
C2A	CB	HIS- 167	4.24	0	Hydrophobic	false
DuAr	DuAr	HIS- 167	3.82	0	Aromatic Face/Face	false
C5A	CB	ASN- 207	4.29	0	Hydrophobic	false
O1P	N	SER- 208	3.09	147.66	H-Bond (Protein Donor)	false
N1	NH1	ARG- 223	3.16	153.4	H-Bond (Protein Donor)	false
O1P	N	GLY- 225	3.13	123.9	H-Bond (Protein Donor)	false
O2P	N	ILE- 226	2.92	147.22	H-Bond (Protein Donor)	false
OG	OH	TYR- 287	3.45	137.79	H-Bond (Protein Donor)	false
O	N	MET- 315	3.2	157.94	H-Bond (Protein Donor)	false
CB	CE2	TYR- 356	3.54	0	Hydrophobic	false