scPDB - 4l7f entry

Protein Data Bank Entry:

PDB ID : 4l7f

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2013-06-13

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:	28.546
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.349	1245.375

% Hydrophobic	% Polar
41.73	58.27
According to VolSite

Ligand :

HET Code:	1V5
Formula:	C26H26FN5O2
Molecular weight:	459.515 g/mol
DrugBank ID:	-
Buried Surface Area:	64.45 %
Polar Surface area:	91.55 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-4.56618	53.1911	4.11026

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
C36	CG2	ILE- 32	4.14	0	Hydrophobic	false
C26	CD1	ILE- 32	4.08	0	Hydrophobic	false
C54	CB	GLN- 37	3.95	0	Hydrophobic	false
C37	CG1	VAL- 40	4.31	0	Hydrophobic	false
C51	CG2	VAL- 40	3.56	0	Hydrophobic	false
C45	CG2	VAL- 40	3.84	0	Hydrophobic	false
C40	CG1	VAL- 40	4.24	0	Hydrophobic	false
C32	CB	ALA- 53	4.49	0	Hydrophobic	false
O30	NZ	LYS- 55	2.96	153.42	H-Bond (Protein Donor)	false
C53	CD	LYS- 55	3.72	0	Hydrophobic	false
F60	CD2	LEU- 57	3.23	0	Hydrophobic	false
C40	CE	MET- 108	4.12	0	Hydrophobic	false
C21	CD1	LEU- 110	4.05	0	Hydrophobic	false
N28	N	MET- 111	2.87	166.73	H-Bond (Protein Donor)	false
N34	O	MET- 111	2.99	147.35	H-Bond (Ligand Donor)	false
C35	CB	ASN- 114	4.38	0	Hydrophobic	false
O17	NE2	GLN- 117	3.04	163.54	H-Bond (Protein Donor)	false
C32	CG1	VAL- 158	4.24	0	Hydrophobic	false
C31	CB	LEU- 168	4.2	0	Hydrophobic	false
C40	CD1	LEU- 168	3.47	0	Hydrophobic	false
C31	CB	ASP- 169	3.92	0	Hydrophobic	false