scPDB - 2ddo entry

Protein Data Bank Entry:

PDB ID : 2ddo

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2006-02-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxine/pyridoxal/pyridoxamine kinase
ID:	PDXK_ECOLI
AC:	P40191
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	52.787
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.174	543.375

% Hydrophobic	% Polar
49.69	50.31
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	61.78 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-5.628	14.3006	47.0241

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
O3G	OE1	GLU- 162	3.17	169.41	H-Bond (Protein Donor)	false
O3'	OG1	THR- 195	3.03	172.73	H-Bond (Protein Donor)	false
C2'	SD	MET- 206	4.27	0	Hydrophobic	false
O2'	NE2	HIS- 221	3.21	169.5	H-Bond (Ligand Donor)	false
N6	O	VAL- 224	2.84	164.83	H-Bond (Ligand Donor)	false
N1	N	VAL- 224	3.03	163.37	H-Bond (Protein Donor)	false
O1A	OG1	THR- 231	2.96	147.32	H-Bond (Protein Donor)	false
C5'	CG	PHE- 235	4.18	0	Hydrophobic	false
C4'	CD1	PHE- 235	3.86	0	Hydrophobic	false
C1'	CG1	VAL- 260	3.78	0	Hydrophobic	false
O3G	MG	MG- 284	2.27	0	Metal Acceptor	false