scPDB - 3fhx entry

Protein Data Bank Entry:

PDB ID : 3fhx

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-12-10

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
A	100 %

Ligand binding site composition:

B-Factor:	43.699
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ATP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.869	759.375

% Hydrophobic	% Polar
52.89	47.11
According to VolSite

Ligand :

HET Code:	PXL
Formula:	C8H9NO3
Molecular weight:	167.162 g/mol
DrugBank ID:	DB00147
Buried Surface Area:	43.77 %
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
30.1197	6.32758	38.5318

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
N1	OG	SER- 12	3.33	149.23	H-Bond (Protein Donor)	false
C2A	CG2	VAL- 41	4.46	0	Hydrophobic	false
C3	CB	HIS- 46	3.93	0	Hydrophobic	false
C3	CG2	THR- 47	4.15	0	Hydrophobic	false
C2A	CG2	THR- 47	4.38	0	Hydrophobic	false
O4A	OG1	THR- 47	3.03	138.6	H-Bond (Protein Donor)	false
O3	N	THR- 47	2.61	174.32	H-Bond (Protein Donor)	false
O3	OG1	THR- 47	3.04	143.67	H-Bond (Protein Donor)	false
C5A	CG1	VAL- 231	4.41	0	Hydrophobic	false