scPDB - 3ka0 entry

Protein Data Bank Entry:

PDB ID : 3ka0

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2009-10-16

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:	61.557
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.720	499.500

% Hydrophobic	% Polar
41.89	58.11
According to VolSite

Ligand :

HET Code:	MK3
Formula:	C20H15N5O2S
Molecular weight:	389.430 g/mol
DrugBank ID:	-
Buried Surface Area:	49.94 %
Polar Surface area:	141.72 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
236.473	82.4359	182.275

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
C3	CG1	VAL- 78	3.35	0	Hydrophobic	false
C6	CG2	VAL- 78	3.59	0	Hydrophobic	false
C12	CG2	VAL- 78	3.28	0	Hydrophobic	false
O2	NE2	GLN- 80	3.3	131.07	H-Bond (Protein Donor)	false
O2	NZ	LYS- 89	3.49	135.3	H-Bond (Protein Donor)	false
C8	CB	ALA- 91	3.45	0	Hydrophobic	false
C7	CB	ALA- 91	3.88	0	Hydrophobic	false
N2	NZ	LYS- 93	2.81	146.66	H-Bond (Protein Donor)	false
C9	CG1	VAL- 118	4.01	0	Hydrophobic	false
C10	CE	MET- 138	4.05	0	Hydrophobic	false
O1	O	GLU- 139	2.7	155	H-Bond (Ligand Donor)	false
C14	SG	CYS- 140	4.31	0	Hydrophobic	false
S1	SG	CYS- 140	3.86	0	Hydrophobic	false
O1	N	LEU- 141	2.87	130.11	H-Bond (Protein Donor)	false
C8	CG	LEU- 141	4.23	0	Hydrophobic	false
C9	CD1	LEU- 141	4.14	0	Hydrophobic	false
C14	CB	LEU- 141	4.46	0	Hydrophobic	false
C5	CD1	LEU- 193	3.84	0	Hydrophobic	false
N1	OG1	THR- 206	2.88	142.81	H-Bond (Protein Donor)	false
C3	CB	ASP- 207	4.45	0	Hydrophobic	false