scPDB - 1rfv entry

Protein Data Bank Entry:

PDB ID : 1rfv

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2003-11-10

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_SHEEP
AC:	P82197
Organism:	Ovis aries
Reign:	Eukaryota
TaxID:	9940
EC Number:	2.7.1.35

Chains:

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

Ligand binding site composition:

B-Factor:	28.972
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.988	1603.125

% Hydrophobic	% Polar
44.84	55.16
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	58.85 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
48.7352	30.6448	42.0427

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
O1B	OG1	THR- 186	2.79	149.21	H-Bond (Protein Donor)	false
C2'	SD	MET- 223	3.97	0	Hydrophobic	false
N6	O	VAL- 226	2.98	158.13	H-Bond (Ligand Donor)	false
N1	N	VAL- 226	2.75	163.47	H-Bond (Protein Donor)	false
O2A	OG1	THR- 233	3.06	136.55	H-Bond (Protein Donor)	false
C3'	CD1	PHE- 237	3.98	0	Hydrophobic	false
C4'	CE	MET- 263	4.44	0	Hydrophobic	false
C1'	CE	MET- 263	3.89	0	Hydrophobic	false
C1'	CD1	LEU- 267	4.14	0	Hydrophobic	false
O2B	ZN	ZN- 1402	2.03	0	Metal Acceptor	false