scPDB - 2vte entry

Protein Data Bank Entry:

PDB ID : 2vte

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2008-05-14

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:	29.871
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.000	1076.625

% Hydrophobic	% Polar
37.30	62.70
According to VolSite

Ligand :

HET Code:	IK4
Formula:	C23H18N2O7S
Molecular weight:	466.463 g/mol
DrugBank ID:	-
Buried Surface Area:	54.4 %
Polar Surface area:	167.83 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-20.5984	1.44285	19.9843

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
N31	N	THR- 36	3.38	156.65	H-Bond (Protein Donor)	false
C28	CG	ARG- 37	4.32	0	Hydrophobic	false
C29	CD	ARG- 37	3.97	0	Hydrophobic	false
DuAr	CZ	ARG- 37	3.73	20.26	Pi/Cation	false
C17	CG	PRO- 72	3.89	0	Hydrophobic	false
CG	CG2	THR- 321	3.84	0	Hydrophobic	false
O	NZ	LYS- 348	3.06	169.98	H-Bond (Protein Donor)	false
O	NZ	LYS- 348	3.06	0	Ionic (Protein Cationic)	false
CG	CB	ALA- 414	3.74	0	Hydrophobic	false
OE1	OG	SER- 415	2.68	146.56	H-Bond (Protein Donor)	false
OE1	N	SER- 415	2.74	160.71	H-Bond (Protein Donor)	false
C21	CD1	LEU- 416	4.36	0	Hydrophobic	false
C14	CD1	LEU- 416	4.48	0	Hydrophobic	false
CB	CD1	LEU- 416	4.29	0	Hydrophobic	false
CG	CG	LEU- 416	4.4	0	Hydrophobic	false
OE2	N	PHE- 422	2.96	139.46	H-Bond (Protein Donor)	false