scPDB - 2jfz entry

Protein Data Bank Entry:

PDB ID : 2jfz

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2007-02-06

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
B	100 %

Ligand binding site composition:

B-Factor:	16.612
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.180	465.750

% Hydrophobic	% Polar
60.87	39.13
According to VolSite

Ligand :

HET Code:	003
Formula:	C26H25N5O2
Molecular weight:	439.509 g/mol
DrugBank ID:	-
Buried Surface Area:	60.57 %
Polar Surface area:	71.33 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
14.9644	90.4315	36.3813

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
C24	CG2	VAL- 10	3.74	0	Hydrophobic	false
C26	CG1	VAL- 10	3.43	0	Hydrophobic	false
C10	CB	PHE- 13	4.31	0	Hydrophobic	false
C30	CB	PHE- 13	4.18	0	Hydrophobic	false
C9	CB	SER- 14	4.49	0	Hydrophobic	false
C31	CB	SER- 14	4.49	0	Hydrophobic	false
C10	CD	LYS- 17	3.52	0	Hydrophobic	false
C33	CG2	ILE- 149	4.3	0	Hydrophobic	false
C27	CG	GLU- 150	3.97	0	Hydrophobic	false
C12	CD1	LEU- 154	4.37	0	Hydrophobic	false
C33	CB	HIS- 183	4.14	0	Hydrophobic	false
C18	CD1	LEU- 186	4.15	0	Hydrophobic	false
C12	CD2	LEU- 186	3.89	0	Hydrophobic	false
C9	CD2	LEU- 186	3.47	0	Hydrophobic	false
C31	CD1	LEU- 186	3.8	0	Hydrophobic	false
C7	CB	TRP- 252	3.84	0	Hydrophobic	false
C12	CZ3	TRP- 252	3.74	0	Hydrophobic	false
DuAr	DuAr	TRP- 252	3.9	0	Aromatic Face/Face	false
C10	CD2	LEU- 253	4.1	0	Hydrophobic	false