scPDB - 2jfh entry

Protein Data Bank Entry:

PDB ID : 2jfh

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2007-02-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramoylalanine--D-glutamate ligase
ID:	MURD_ECOLI
AC:	P14900
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.3.2.9

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	13.686
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.760	1076.625

% Hydrophobic	% Polar
34.48	65.52
According to VolSite

Ligand :

HET Code:	LK1
Formula:	C19H21NO7S
Molecular weight:	407.438 g/mol
DrugBank ID:	DB08105
Buried Surface Area:	49.77 %
Polar Surface area:	144.04 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
20.9934	-1.90371	20.3907

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
C26	CG2	ILE- 11	4.06	0	Hydrophobic	false
C26	CG2	THR- 36	3.78	0	Hydrophobic	false
C23	CD	ARG- 37	4.35	0	Hydrophobic	false
CG	CG2	THR- 321	4	0	Hydrophobic	false
OXT	NZ	LYS- 348	2.68	168.57	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 348	2.68	0	Ionic (Protein Cationic)	false
O	NZ	LYS- 348	3.61	0	Ionic (Protein Cationic)	false
CB	CB	ALA- 414	4.03	0	Hydrophobic	false
OE2	OG	SER- 415	2.81	169.91	H-Bond (Protein Donor)	false
OE2	N	SER- 415	2.73	173.12	H-Bond (Protein Donor)	false
CB	CG	LEU- 416	3.95	0	Hydrophobic	false
C16	CD1	LEU- 416	3.68	0	Hydrophobic	false
CG	CD1	PHE- 422	4.32	0	Hydrophobic	false
OE1	N	PHE- 422	2.7	134.57	H-Bond (Protein Donor)	false