scPDB - 3dv3 entry

Protein Data Bank Entry:

PDB ID : 3dv3

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-07-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dual specificity mitogen-activated protein kinase kinase 1
ID:	MP2K1_HUMAN
AC:	Q02750
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.12.2

Chains:

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

Ligand binding site composition:

B-Factor:	53.209
Number of residues:	42
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:	ATP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.127	499.500

% Hydrophobic	% Polar
54.05	45.95
According to VolSite

Ligand :

HET Code:	MEK
Formula:	C18H18F3IN2O5
Molecular weight:	526.246 g/mol
DrugBank ID:	-
Buried Surface Area:	74.04 %
Polar Surface area:	100.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
39.4663	-13.835	0.24669

Binding mode :

What is Poseview ?

2D View
3D View

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	CD	LYS- 97	4.34	0	Hydrophobic	false
O1	NZ	LYS- 97	3.05	128.33	H-Bond (Protein Donor)	false
O2	NZ	LYS- 97	3.34	145.95	H-Bond (Protein Donor)	false
O3	NZ	LYS- 97	3.48	134.21	H-Bond (Protein Donor)	false
F2	CD2	LEU- 115	3.5	0	Hydrophobic	false
F2	CD1	LEU- 118	4.31	0	Hydrophobic	false
I1	CD2	LEU- 118	4.42	0	Hydrophobic	false
C3	CD1	LEU- 118	3.84	0	Hydrophobic	false
I1	CB	VAL- 127	4	0	Hydrophobic	false
C1	CD1	ILE- 141	4.04	0	Hydrophobic	false
F1	CD1	ILE- 141	3.73	0	Hydrophobic	false
C6	CG2	ILE- 141	4.04	0	Hydrophobic	false
C12	CD1	ILE- 141	4.19	0	Hydrophobic	false
C5	SD	MET- 143	3.63	0	Hydrophobic	false
F1	CE	MET- 143	3.57	0	Hydrophobic	false
C18	CB	ARG- 189	3.88	0	Hydrophobic	false
C18	CB	ASP- 190	4.23	0	Hydrophobic	false
I1	CB	CYS- 207	4.48	0	Hydrophobic	false
C4	CB	CYS- 207	4.3	0	Hydrophobic	false
I1	CE2	PHE- 209	4.12	0	Hydrophobic	false
F2	CB	VAL- 211	4.49	0	Hydrophobic	false
C2	CG2	VAL- 211	4.39	0	Hydrophobic	false
F3	CG2	VAL- 211	3.83	0	Hydrophobic	false
F3	CB	SER- 212	4.03	0	Hydrophobic	false
C16	CG	LEU- 215	3.89	0	Hydrophobic	false
C8	CD2	LEU- 215	4.18	0	Hydrophobic	false
C10	CD2	LEU- 215	3.41	0	Hydrophobic	false
C17	CG1	ILE- 216	3.91	0	Hydrophobic	false
C16	CG1	ILE- 216	3.95	0	Hydrophobic	false
C16	CG	MET- 219	4.38	0	Hydrophobic	false
C14	CE	MET- 219	3.95	0	Hydrophobic	false
N1	O	HOH- 9008	2.83	138.94	H-Bond (Ligand Donor)	false
O5	O	HOH- 9085	3.5	146.72	H-Bond (Protein Donor)	false