scPDB - 2v34 entry

Protein Data Bank Entry:

PDB ID : 2v34

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-06-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
ID:	ISPE_AQUAE
AC:	O67060
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	28.462
Number of residues:	19
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.092	843.750

% Hydrophobic	% Polar
48.40	51.60
According to VolSite

Ligand :

HET Code:	CTN
Formula:	C9H13N3O5
Molecular weight:	243.217 g/mol
DrugBank ID:	DB02097
Buried Surface Area:	52.08 %
Polar Surface area:	128.61 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
94.0125	49.0788	16.5312

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
C1'	CD2	TYR- 24	4.45	0	Hydrophobic	false
C3'	CE2	TYR- 24	3.66	0	Hydrophobic	false
N3	N	HIS- 25	3.03	140.1	H-Bond (Protein Donor)	false
O2	ND1	HIS- 25	2.77	170.45	H-Bond (Protein Donor)	false
N4	O	HIS- 25	3.1	165.05	H-Bond (Ligand Donor)	false
N4	O	LYS- 145	3.05	154.59	H-Bond (Ligand Donor)	false
C5'	CB	THR- 171	4.12	0	Hydrophobic	false
C4'	CG2	THR- 171	4.37	0	Hydrophobic	false
C1'	CG2	THR- 171	4.5	0	Hydrophobic	false
C1'	CD1	TYR- 175	3.58	0	Hydrophobic	false