scPDB - 2hdn entry

Protein Data Bank Entry:

PDB ID : 2hdn

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2006-06-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Elongation factor Tu 1
ID:	EFTU1_ECOLI
AC:	P0CE47
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	22 %
C	19 %
B	41 %
D	19 %

Ligand binding site composition:

B-Factor:	30.376
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:	GDP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.772	270.000

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	TAC
Formula:	C22H22N2O8
Molecular weight:	442.419 g/mol
DrugBank ID:	DB00759
Buried Surface Area:	32.59 %
Polar Surface area:	191.3 Å2

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

Mass center Coordinates

X	Y	Z
53.6968	18.5839	97.6177

Binding mode :

What is Poseview ?

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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
C8	CB	SER- 65	4.44	0	Hydrophobic	false
C9	CB	SER- 65	3.54	0	Hydrophobic	false
O10	O	ASP- 80	2.78	165.21	H-Bond (Ligand Donor)	false
C9	CG	PRO- 82	4.31	0	Hydrophobic	false
C1A	CB	PRO- 82	3.81	0	Hydrophobic	false
O11	MG	MG- 1998	2.37	0	Metal Acceptor	false
O12	MG	MG- 1998	2.09	0	Metal Acceptor	false
O1C	O2A	GDP- 1999	2.63	136.49	H-Bond (Ligand Donor)	false