scPDB - 2yxu entry

Protein Data Bank Entry:

PDB ID : 2yxu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-04-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal kinase
ID:	PDXK_HUMAN
AC:	O00764
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.35

Chains:

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

Ligand binding site composition:

B-Factor:	33.386
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG NA

Cavity properties

Ligandability	Volume (Å3)
1.086	1005.750

% Hydrophobic	% Polar
40.94	59.06
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	66.38 %
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
1.47245	27.1635	24.1577

Binding mode :

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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
O1G	OD2	ASP- 113	2.67	165.36	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 150	3.05	164.51	H-Bond (Protein Donor)	false
O1G	OE1	GLU- 153	2.86	163.62	H-Bond (Protein Donor)	false
C5'	CB	THR- 186	4.21	0	Hydrophobic	false
O2B	OG	SER- 187	2.75	176.05	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 199	4.05	0	Hydrophobic	false
N6	O	VAL- 226	3.16	161.14	H-Bond (Ligand Donor)	false
N1	N	VAL- 226	2.67	144.23	H-Bond (Protein Donor)	false
O1A	OG1	THR- 233	2.74	138.87	H-Bond (Protein Donor)	false
C4'	CD1	PHE- 237	4.01	0	Hydrophobic	false
C4'	CD1	LEU- 263	4.13	0	Hydrophobic	false
C1'	CD2	LEU- 263	4.22	0	Hydrophobic	false
C1'	CD1	LEU- 267	4.1	0	Hydrophobic	false
O1B	MG	MG- 2404	1.97	0	Metal Acceptor	false
O2A	MG	MG- 2404	2.22	0	Metal Acceptor	false