scPDB - 2w4i entry

Protein Data Bank Entry:

PDB ID : 2w4i

Resolution :1.870 Å

Experimental Method : X-ray

Deposition Date : 2008-11-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate racemase
ID:	MURI_HELPJ
AC:	Q9ZLT0
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85963
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	48 %
F	52 %

Ligand binding site composition:

B-Factor:	10.486
Number of residues:	36
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.423	1069.875

% Hydrophobic	% Polar
57.10	42.90
According to VolSite

Ligand :

HET Code:	VGA
Formula:	C22H20N3OS
Molecular weight:	374.479 g/mol
DrugBank ID:	DB08698
Buried Surface Area:	73.79 %
Polar Surface area:	78.03 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
39.718	18.4433	55.2319

Binding mode :

What is Poseview ?

2D View
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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
C9	CG2	VAL- 37	3.88	0	Hydrophobic	false
C6	CG	PRO- 38	4.42	0	Hydrophobic	false
C11	CG	PRO- 38	4.49	0	Hydrophobic	false
S23	CB	PRO- 38	3.8	0	Hydrophobic	false
C8	CB	PRO- 38	3.36	0	Hydrophobic	false
C14	CG2	THR- 41	3.73	0	Hydrophobic	false
C17	CG2	THR- 41	3.67	0	Hydrophobic	false
C14	CB	SER- 143	4.49	0	Hydrophobic	false
C18	CB	SER- 143	3.75	0	Hydrophobic	false
C15	CD2	LEU- 144	4.06	0	Hydrophobic	false
C19	CD2	LEU- 144	4.07	0	Hydrophobic	false
C8	CB	VAL- 146	4.14	0	Hydrophobic	false
C9	CG1	VAL- 146	3.55	0	Hydrophobic	false
S23	CG1	VAL- 146	3.31	0	Hydrophobic	false
C6	CB	PRO- 147	4.31	0	Hydrophobic	false
C14	CG	PRO- 147	4.15	0	Hydrophobic	false
S23	CB	PRO- 147	4.48	0	Hydrophobic	false
C16	CB	PRO- 147	3.49	0	Hydrophobic	false
C17	CG	PRO- 147	3.94	0	Hydrophobic	false
C20	CB	PRO- 147	3.98	0	Hydrophobic	false
C12	CB	PRO- 147	3.55	0	Hydrophobic	false
S23	CG	GLU- 150	4.37	0	Hydrophobic	false
C10	CG	GLU- 150	3.66	0	Hydrophobic	false
C16	CB	GLU- 150	4.16	0	Hydrophobic	false
C20	CB	GLU- 150	3.88	0	Hydrophobic	false
C15	CG	GLU- 151	3.77	0	Hydrophobic	false
C19	CG	GLU- 151	3.62	0	Hydrophobic	false
O27	OE2	GLU- 151	2.71	132.62	H-Bond (Ligand Donor)	false