scPDB - 2y67 entry

Protein Data Bank Entry:

PDB ID : 2y67

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-01-20

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:	36.127
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.231	536.625

% Hydrophobic	% Polar
43.40	56.60
According to VolSite

Ligand :

HET Code:	N21
Formula:	C22H17N2O9S2
Molecular weight:	517.508 g/mol
DrugBank ID:	-
Buried Surface Area:	54.15 %
Polar Surface area:	217.58 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
45.2406	0.893371	19.2642

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
OBH	N	THR- 36	3.09	151.26	H-Bond (Protein Donor)	false
CAH	CD	ARG- 37	4.19	0	Hydrophobic	false
CAC	CB	SER- 71	4.27	0	Hydrophobic	false
SBG	CB	SER- 71	4.48	0	Hydrophobic	false
CAQ	CG	PRO- 72	4.05	0	Hydrophobic	false
CG	CG2	THR- 321	4.35	0	Hydrophobic	false
OXT	NZ	LYS- 348	2.95	161.16	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 348	2.95	0	Ionic (Protein Cationic)	false
O	NZ	LYS- 348	3.9	0	Ionic (Protein Cationic)	false
CG	CB	ALA- 414	3.7	0	Hydrophobic	false
OE1	OG	SER- 415	2.56	148.01	H-Bond (Protein Donor)	false
OE1	N	SER- 415	2.77	169.77	H-Bond (Protein Donor)	false
CG	CG	LEU- 416	4.1	0	Hydrophobic	false
OE2	N	PHE- 422	2.93	145.37	H-Bond (Protein Donor)	false