scPDB - 3v04 entry

Protein Data Bank Entry:

PDB ID : 3v04

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-12-07

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:	67.817
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:	ATP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.960	924.750

% Hydrophobic	% Polar
47.08	52.92
According to VolSite

Ligand :

HET Code:	V04
Formula:	C16H14FIN4O3
Molecular weight:	456.210 g/mol
DrugBank ID:	-
Buried Surface Area:	71.42 %
Polar Surface area:	99.27 Å2

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

Mass center Coordinates

X	Y	Z
33.0623	-29.2958	-27.4051

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
O3	N	GLY- 80	3.11	146.64	H-Bond (Protein Donor)	false
F1	CD	LYS- 97	3.48	0	Hydrophobic	false
C16	CD	LYS- 97	4.14	0	Hydrophobic	false
O1	NZ	LYS- 97	2.86	157.32	H-Bond (Protein Donor)	false
O2	NZ	LYS- 97	3.24	125.93	H-Bond (Protein Donor)	false
I1	CD2	LEU- 118	4.35	0	Hydrophobic	false
C10	CD2	LEU- 118	3.98	0	Hydrophobic	false
C11	CD1	LEU- 118	4.18	0	Hydrophobic	false
I1	CB	VAL- 127	4.1	0	Hydrophobic	false
F1	CD1	ILE- 141	3.6	0	Hydrophobic	false
C4	CD1	ILE- 141	4.36	0	Hydrophobic	false
C8	CD1	ILE- 141	4.01	0	Hydrophobic	false
C13	CG2	ILE- 141	3.9	0	Hydrophobic	false
F1	CE	MET- 143	3.88	0	Hydrophobic	false
C12	SD	MET- 143	3.8	0	Hydrophobic	false
C1	CB	ASP- 208	4.47	0	Hydrophobic	false
I1	CZ	PHE- 209	3.93	0	Hydrophobic	false
N2	N	VAL- 211	3.27	122.33	H-Bond (Protein Donor)	false
N1	O	SER- 212	3.43	136.08	H-Bond (Ligand Donor)	false
N2	N	SER- 212	3.36	133.94	H-Bond (Protein Donor)	false
C6	CD1	LEU- 215	3.61	0	Hydrophobic	false
C3	CG1	ILE- 216	4.33	0	Hydrophobic	false
C2	CE	MET- 219	3.7	0	Hydrophobic	false
O3	O1A	ATP- 502	3.27	158.06	H-Bond (Ligand Donor)	false