scPDB - 2xpc entry

Protein Data Bank Entry:

PDB ID : 2xpc

Resolution :1.490 Å

Experimental Method : X-ray

Deposition Date : 2010-08-26

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:	19.732
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.541	465.750

% Hydrophobic	% Polar
42.03	57.97
According to VolSite

Ligand :

HET Code:	051
Formula:	C26H21FN2O7S
Molecular weight:	524.518 g/mol
DrugBank ID:	-
Buried Surface Area:	54.57 %
Polar Surface area:	167.83 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.1216	31.2273	48.5586

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
N30	N	THR- 36	3.05	167.16	H-Bond (Protein Donor)	false
F25	CD	ARG- 37	3.35	0	Hydrophobic	false
C29	CB	SER- 71	3.58	0	Hydrophobic	false
C19	CG	PRO- 72	4.02	0	Hydrophobic	false
C5	CG2	THR- 321	3.96	0	Hydrophobic	false
O1	NZ	LYS- 348	3.81	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 348	2.69	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 348	2.69	171.77	H-Bond (Protein Donor)	false
C5	CB	ALA- 414	3.86	0	Hydrophobic	false
O3	OG	SER- 415	2.81	157.68	H-Bond (Protein Donor)	false
O3	N	SER- 415	2.95	155.66	H-Bond (Protein Donor)	false
C6	CD1	LEU- 416	3.84	0	Hydrophobic	false
C14	CD1	LEU- 416	3.76	0	Hydrophobic	false
C4	CD2	PHE- 422	4.38	0	Hydrophobic	false
O4	N	PHE- 422	2.75	141.35	H-Bond (Protein Donor)	false
O32	O	HOH- 2245	2.85	179.95	H-Bond (Protein Donor)	false