scPDB - 3v3v entry

Protein Data Bank Entry:

PDB ID : 3v3v

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mitogen-activated protein kinase 8
ID:	MK08_HUMAN
AC:	P45983
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.24

Chains:

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

Ligand binding site composition:

B-Factor:	58.255
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.941	442.125

% Hydrophobic	% Polar
51.91	48.09
According to VolSite

Ligand :

HET Code:	MYU
Formula:	C15H8O8
Molecular weight:	316.219 g/mol
DrugBank ID:	-
Buried Surface Area:	66.25 %
Polar Surface area:	153.34 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
31.2127	44.3929	4.15448

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
C1	CG2	VAL- 40	3.69	0	Hydrophobic	false
O18	NZ	LYS- 55	2.76	142.58	H-Bond (Protein Donor)	false
C3	CD	LYS- 55	4.01	0	Hydrophobic	false
O18	OE2	GLU- 73	3.19	143.17	H-Bond (Ligand Donor)	false
C5	SD	MET- 108	3.73	0	Hydrophobic	false
O20	O	GLU- 109	2.93	129.74	H-Bond (Ligand Donor)	false
O21	N	MET- 111	2.7	121.83	H-Bond (Protein Donor)	false
C5	CD2	LEU- 168	3.42	0	Hydrophobic	false
C2	CD1	LEU- 168	4.13	0	Hydrophobic	false
C3	CB	ASP- 169	3.79	0	Hydrophobic	false