scPDB - 2jfg entry

Protein Data Bank Entry:

PDB ID : 2jfg

Resolution :1.520 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:	9.420
Number of residues:	55
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.193	1164.375

% Hydrophobic	% Polar
44.06	55.94
According to VolSite

Ligand :

HET Code:	UMA
Formula:	C23H33N4O20P2
Molecular weight:	747.470 g/mol
DrugBank ID:	DB01673
Buried Surface Area:	55.39 %
Polar Surface area:	383.92 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
31.6524	13.4481	17.9083

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
O1B	N	LEU- 15	3.24	155.81	H-Bond (Protein Donor)	false
O2B	N	THR- 16	2.85	160.87	H-Bond (Protein Donor)	false
O2B	OG1	THR- 16	2.72	153.01	H-Bond (Protein Donor)	false
N3	OG1	THR- 36	2.7	168.81	H-Bond (Ligand Donor)	false
O4	N	THR- 36	2.97	165.25	H-Bond (Protein Donor)	false
C1B	CD	ARG- 37	4.1	0	Hydrophobic	false
O2A	NH2	ARG- 37	3.28	127.47	H-Bond (Protein Donor)	false
C1'	CG	PRO- 72	3.83	0	Hydrophobic	false
O1A	N	GLY- 73	2.8	131.89	H-Bond (Protein Donor)	false
O4'	O	ASN- 138	2.73	131.69	H-Bond (Ligand Donor)	false
N4	OD1	ASN- 138	3.07	161.03	H-Bond (Ligand Donor)	false
O20	ND2	ASN- 138	3.02	171.19	H-Bond (Protein Donor)	false
C6'	CG	PRO- 142	4.41	0	Hydrophobic	false
C23	CB	SER- 159	3.61	0	Hydrophobic	false
C8'	CE2	PHE- 161	4.45	0	Hydrophobic	false
C23	CD2	PHE- 161	3.83	0	Hydrophobic	false
C4B	CD1	LEU- 416	3.96	0	Hydrophobic	false
C20	CE2	PHE- 422	3.77	0	Hydrophobic	false
O6'	O	HOH- 2142	2.9	154.37	H-Bond (Ligand Donor)	false
O2A	O	HOH- 2471	2.77	179.96	H-Bond (Protein Donor)	false