scPDB - 4fv8 entry

Protein Data Bank Entry:

PDB ID : 4fv8

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-06-29

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:	17.517
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.875	546.750

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	E63
Formula:	C23H21N9O
Molecular weight:	439.473 g/mol
DrugBank ID:	-
Buried Surface Area:	58.91 %
Polar Surface area:	131.68 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-17.3417	3.04506	16.2004

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
C15	CG2	ILE- 29	4.47	0	Hydrophobic	false
C16	CD1	ILE- 29	4.44	0	Hydrophobic	false
C21	CG1	ILE- 29	3.97	0	Hydrophobic	false
C13	CG1	VAL- 37	4.05	0	Hydrophobic	false
C12	CB	ALA- 50	3.72	0	Hydrophobic	false
C12	CB	GLN- 103	4.24	0	Hydrophobic	false
N7	O	ASP- 104	2.73	139.63	H-Bond (Ligand Donor)	false
C17	CD1	LEU- 105	4.06	0	Hydrophobic	false
N8	O	MET- 106	2.82	149.44	H-Bond (Ligand Donor)	false
N5	O	MET- 106	3.17	140.86	H-Bond (Ligand Donor)	false
N6	N	MET- 106	3.07	164.65	H-Bond (Protein Donor)	false
N3	OD2	ASP- 109	2.71	148.23	H-Bond (Ligand Donor)	false
N9	NZ	LYS- 112	2.83	156.33	H-Bond (Protein Donor)	false
C12	CD1	LEU- 154	3.98	0	Hydrophobic	false
C14	SG	CYS- 164	4.2	0	Hydrophobic	false
N1	OD2	ASP- 165	2.75	147.91	H-Bond (Ligand Donor)	false
O	O	HOH- 541	2.73	125.89	H-Bond (Protein Donor)	false