scPDB - 3kga entry

Protein Data Bank Entry:

PDB ID : 3kga

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2009-10-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	MAP kinase-activated protein kinase 2
ID:	MAPK2_HUMAN
AC:	P49137
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	42.928
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.142	519.750

% Hydrophobic	% Polar
53.90	46.10
According to VolSite

Ligand :

HET Code:	LX9
Formula:	C26H21N5O
Molecular weight:	419.478 g/mol
DrugBank ID:	-
Buried Surface Area:	61.49 %
Polar Surface area:	88.72 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
36.912	6.08559	13.8027

Binding mode :

What is Poseview ?

2D View
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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
C30	CD2	LEU- 70	3.47	0	Hydrophobic	false
C33	CG	LEU- 70	3.7	0	Hydrophobic	false
C40	CD2	LEU- 70	3.38	0	Hydrophobic	false
C7	CG1	VAL- 78	4.17	0	Hydrophobic	false
C12	CG2	VAL- 78	3.79	0	Hydrophobic	false
C42	CG	GLN- 80	3.54	0	Hydrophobic	false
C42	CB	LYS- 89	4.15	0	Hydrophobic	false
C49	CD	LYS- 89	3.95	0	Hydrophobic	false
N43	O	PHE- 90	2.91	156.67	H-Bond (Ligand Donor)	false
O25	NZ	LYS- 93	2.74	172.67	H-Bond (Protein Donor)	false
C14	SD	MET- 138	3.91	0	Hydrophobic	false
N26	O	GLU- 139	2.87	164.37	H-Bond (Ligand Donor)	false
C39	SG	CYS- 140	3.74	0	Hydrophobic	false
N2	N	LEU- 141	2.97	145.29	H-Bond (Protein Donor)	false
C8	CD1	LEU- 193	3.69	0	Hydrophobic	false
C11	CB	THR- 206	4.04	0	Hydrophobic	false
N17	OD2	ASP- 207	3.03	164.16	H-Bond (Ligand Donor)	false