scPDB - 1td2 entry

Protein Data Bank Entry:

PDB ID : 1td2

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2004-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal kinase PdxY
ID:	PDXY_ECOLI
AC:	P77150
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.141
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.281	759.375

% Hydrophobic	% Polar
57.78	42.22
According to VolSite

Ligand :

HET Code:	PXL
Formula:	C8H9NO3
Molecular weight:	167.162 g/mol
DrugBank ID:	DB00147
Buried Surface Area:	72.7 %
Polar Surface area:	70.42 Å2

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

Mass center Coordinates

X	Y	Z
0.9075	-2.56425	6.20075

Binding mode :

What is Poseview ?

2D View
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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
N1	OG	SER- 10	2.61	176.91	H-Bond (Protein Donor)	false
C2A	CB	SER- 10	4.08	0	Hydrophobic	false
C2A	CG1	VAL- 12	4.19	0	Hydrophobic	false
C3	CB	ALA- 17	4.25	0	Hydrophobic	false
C2A	CD1	PHE- 41	3.87	0	Hydrophobic	false
C3	CB	HIS- 44	4.03	0	Hydrophobic	false
C2A	CB	HIS- 44	4.29	0	Hydrophobic	false
O3	N	THR- 45	2.85	156.11	H-Bond (Protein Donor)	false
C2A	CG2	THR- 45	4.48	0	Hydrophobic	false
C5	CB	TYR- 83	4.37	0	Hydrophobic	false
C2A	CZ	TYR- 83	4.26	0	Hydrophobic	false
C5A	CG1	VAL- 114	4.14	0	Hydrophobic	false
C4	SG	CYS- 122	3.72	0	Hydrophobic	false
C5	CG1	VAL- 220	4.29	0	Hydrophobic	false
C4	CG1	VAL- 220	3.84	0	Hydrophobic	false
OP4	OD2	ASP- 224	2.76	170.08	H-Bond (Ligand Donor)	false