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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3v01

2.710 Å

X-ray

2011-12-07

Interactomes:
Molecular Function:
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
A100 %


Ligand binding site composition:

B-Factor:75.404
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors: ATP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.1021015.875

% Hydrophobic% Polar
46.1853.82
According to VolSite

Ligand :
3v01_1 Structure
HET Code: 3V0
Formula: C17H15FIN3O5
Molecular weight: 487.221 g/mol
DrugBank ID: -
Buried Surface Area:71.82 %
Polar Surface area: 116.85 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
32.540829.3258-15.0044


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
F1CDLYS- 973.420Hydrophobic
O2NZLYS- 972.7156.27H-Bond
(Protein Donor)
O3NZLYS- 973.37125.7H-Bond
(Protein Donor)
I1CD2LEU- 1184.420Hydrophobic
C11CD1LEU- 1184.040Hydrophobic
I1CBVAL- 1274.120Hydrophobic
C9CD1ILE- 1414.150Hydrophobic
F1CG2ILE- 1413.680Hydrophobic
F1CEMET- 1433.750Hydrophobic
C13SDMET- 1433.750Hydrophobic
I1CE2PHE- 2093.90Hydrophobic
N1NSER- 2123.09173.92H-Bond
(Protein Donor)
C2CD1LEU- 2153.990Hydrophobic
C4CD1LEU- 2153.670Hydrophobic
C2CG1ILE- 2163.770Hydrophobic
O4O1AATP- 5023.05170.92H-Bond
(Ligand Donor)