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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:

3wi6

2.990 Å

X-ray

2013-09-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:MAP kinase-activated protein kinase 2
ID:MAPK2_HUMAN
AC:P49137
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:74.827
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.040560.250

% Hydrophobic% Polar
55.4244.58
According to VolSite

Ligand :
3wi6_1 Structure
HET Code: YRZ
Formula: C13H19N6
Molecular weight: 259.330 g/mol
DrugBank ID: -
Buried Surface Area:59.85 %
Polar Surface area: 70.86 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-36.2365-17.4445-13.8768


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- 704.020Hydrophobic
C11CG2VAL- 784.130Hydrophobic
N16NLEU- 1413.26167.5H-Bond
(Protein Donor)
N8OGLU- 1902.99149.29H-Bond
(Ligand Donor)
C5CD1LEU- 1933.770Hydrophobic
N8OD2ASP- 2073.08159.59H-Bond
(Ligand Donor)
N8OD2ASP- 2073.080Ionic
(Ligand Cationic)
N8OD1ASP- 2073.870Ionic
(Ligand Cationic)