scPDB - 1ygj entry

Protein Data Bank Entry:

PDB ID : 1ygj

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2005-01-05

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
A	100 %

Ligand binding site composition:

B-Factor:	29.130
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.301	712.125

% Hydrophobic	% Polar
58.77	41.23
According to VolSite

Ligand :

HET Code:	RMC
Formula:	C20H28N6O
Molecular weight:	368.476 g/mol
DrugBank ID:	DB04776
Buried Surface Area:	55.9 %
Polar Surface area:	79.1 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.6133	57.7768	36.1566

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
NAO	OG	SER- 12	2.76	146.56	H-Bond (Protein Donor)	false
CAD	CB	SER- 12	3.99	0	Hydrophobic	false
CBB	CG1	VAL- 14	3.35	0	Hydrophobic	false
CBB	CG1	VAL- 19	3.67	0	Hydrophobic	false
CBA	CG2	VAL- 19	3.67	0	Hydrophobic	false
CAB	CG2	VAL- 41	3.83	0	Hydrophobic	false
CAF	CD1	PHE- 43	3.26	0	Hydrophobic	false
CAC	CB	PHE- 43	3.76	0	Hydrophobic	false
CBB	CB	HIS- 46	3.82	0	Hydrophobic	false
NAS	OG1	THR- 47	2.68	148.84	H-Bond (Ligand Donor)	false
NAL	N	THR- 47	3.34	173.06	H-Bond (Protein Donor)	false
CAF	CG2	THR- 47	3.98	0	Hydrophobic	false
CAY	CB	TYR- 84	3.52	0	Hydrophobic	false
CAG	CD	ARG- 86	4.15	0	Hydrophobic	false
CAY	CG1	VAL- 115	4.13	0	Hydrophobic	false
CAR	CG1	VAL- 231	4.31	0	Hydrophobic	false
CBA	CG1	VAL- 231	4.33	0	Hydrophobic	false