scPDB - 4g6o entry

Protein Data Bank Entry:

PDB ID : 4g6o

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-07-19

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 1
ID:	MK01_HUMAN
AC:	P28482
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:	44.817
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.059	523.125

% Hydrophobic	% Polar
44.52	55.48
According to VolSite

Ligand :

HET Code:	E28
Formula:	C25H23F3N5O2
Molecular weight:	482.478 g/mol
DrugBank ID:	-
Buried Surface Area:	54.54 %
Polar Surface area:	110.44 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.8303	7.00866	16.4601

Binding mode :

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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
F1	CG2	ILE- 29	4.08	0	Hydrophobic	false
C3	CG2	ILE- 29	3.86	0	Hydrophobic	false
C22	CA	TYR- 34	4.09	0	Hydrophobic	false
C21	CG2	VAL- 37	4.08	0	Hydrophobic	false
C3	CG1	VAL- 37	3.99	0	Hydrophobic	false
F1	CB	VAL- 37	3.68	0	Hydrophobic	false
F2	CG2	VAL- 37	3.69	0	Hydrophobic	false
O1	NZ	LYS- 52	2.73	161.53	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 52	3.89	160.69	Pi/Cation	false
C20	CD	LYS- 52	3.63	0	Hydrophobic	false
C19	CD	LYS- 52	3.66	0	Hydrophobic	false
C22	CG2	ILE- 54	4.04	0	Hydrophobic	false
N4	OE1	GLN- 103	2.52	149.42	H-Bond (Ligand Donor)	false
N3	O	ASP- 104	3.06	134.75	H-Bond (Ligand Donor)	false
N2	N	MET- 106	3.01	149.98	H-Bond (Protein Donor)	false
C5	CD2	LEU- 154	4.09	0	Hydrophobic	false
O1	O	HOH- 585	2.89	179.97	H-Bond (Protein Donor)	false