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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:

3she

2.250 Å

X-ray

2011-06-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:MAP kinase-activated protein kinase 3
ID:MAPK3_HUMAN
AC:Q16644
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:72.780
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.963580.500

% Hydrophobic% Polar
49.4250.58
According to VolSite

Ligand :
3she_1 Structure
HET Code: I85
Formula: C24H23F3N5O2
Molecular weight: 470.467 g/mol
DrugBank ID: -
Buried Surface Area:58.32 %
Polar Surface area: 103.48 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 4
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
14.347111.168314.9402


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
C4CBLEU- 504.190Hydrophobic
C25CD1LEU- 503.620Hydrophobic
C7CG2VAL- 584.460Hydrophobic
C18CG1VAL- 584.010Hydrophobic
C19CBALA- 713.910Hydrophobic
O13NZLYS- 732.87176.99H-Bond
(Protein Donor)
C19SDMET- 1183.970Hydrophobic
C25SGCYS- 1203.820Hydrophobic
N5NMET- 1212.97169.36H-Bond
(Protein Donor)
C26CBGLU- 1223.620Hydrophobic
N2OGLU- 1703.31127.13H-Bond
(Ligand Donor)
C18CD1LEU- 1733.840Hydrophobic
C19CG2THR- 1864.210Hydrophobic
N8OD1ASP- 1873.01123.19H-Bond
(Ligand Donor)