scPDB - 2vag entry

Protein Data Bank Entry:

PDB ID : 2vag

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dual specificity protein kinase CLK1
ID:	CLK1_HUMAN
AC:	P49759
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.12.1

Chains:

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

Ligand binding site composition:

B-Factor:	15.348
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.280	455.625

% Hydrophobic	% Polar
61.48	38.52
According to VolSite

Ligand :

HET Code:	V25
Formula:	C15H14Cl2N3O2
Molecular weight:	339.197 g/mol
DrugBank ID:	DB08691
Buried Surface Area:	73.45 %
Polar Surface area:	82.66 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
7.19155	13.8236	21.3077

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
CAB	CB	LEU- 167	3.64	0	Hydrophobic	false
CL1	CD1	LEU- 167	3.63	0	Hydrophobic	false
CAA	CE2	PHE- 172	4.16	0	Hydrophobic	false
CAL	CZ	PHE- 172	4.46	0	Hydrophobic	false
CAB	CG1	VAL- 175	3.92	0	Hydrophobic	false
CL1	CG1	VAL- 175	4.17	0	Hydrophobic	false
CAT	CG2	VAL- 175	4.07	0	Hydrophobic	false
CAU	CG1	VAL- 175	3.88	0	Hydrophobic	false
CL2	CB	ALA- 189	3.61	0	Hydrophobic	false
CL1	CB	ALA- 189	3.65	0	Hydrophobic	false
NAC	NZ	LYS- 191	2.74	163.05	H-Bond (Protein Donor)	false
CAJ	CG2	VAL- 225	3.91	0	Hydrophobic	false
CL2	CB	PHE- 241	3.52	0	Hydrophobic	false
CL1	CB	LEU- 244	4.43	0	Hydrophobic	false
CAP	CD1	LEU- 244	4.38	0	Hydrophobic	false
CL2	CG	LEU- 244	3.8	0	Hydrophobic	false
CAA	CG	GLU- 292	3.95	0	Hydrophobic	false
NAD	O	GLU- 292	3.01	129.27	H-Bond (Ligand Donor)	false
NAD	OD1	ASN- 293	3.26	125.35	H-Bond (Ligand Donor)	false
CAB	CD2	LEU- 295	4.19	0	Hydrophobic	false
CL1	CD2	LEU- 295	3.87	0	Hydrophobic	false
CAQ	CD2	LEU- 295	3.34	0	Hydrophobic	false
CAJ	CG1	VAL- 324	3.88	0	Hydrophobic	false
CAK	CB	VAL- 324	3.73	0	Hydrophobic	false
CAT	CG2	VAL- 324	4.14	0	Hydrophobic	false