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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:

4zme

1.980 Å

X-ray

2015-05-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Myosin heavy chain kinase A
ID:MHCKA_DICDI
AC:P42527
Organism:Dictyostelium discoideum
Reign:Eukaryota
TaxID:44689
EC Number:2.7.11.7


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:36.839
Number of residues:21
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.328695.250

% Hydrophobic% Polar
44.1755.83
According to VolSite

Ligand :
4zme_2 Structure
HET Code: ADN
Formula: C10H13N5O4
Molecular weight: 267.241 g/mol
DrugBank ID: DB00640
Buried Surface Area:57.19 %
Polar Surface area: 139.54 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
21.3165-11.9541-45.6972


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
C1'CE2PHE- 5864.40Hydrophobic
C4'CBALA- 5874.070Hydrophobic
C1'CBALA- 5874.070Hydrophobic
N7NZLYS- 6453.05144.71H-Bond
(Protein Donor)
N6OE1GLU- 7132.85167.82H-Bond
(Ligand Donor)
N6OPRO- 7142.92150.81H-Bond
(Ligand Donor)
N1NLEU- 7162.94166.46H-Bond
(Protein Donor)
C3'CE1PHE- 7203.930Hydrophobic
C2'CGPHE- 7203.590Hydrophobic
C1'CD2PHE- 7204.380Hydrophobic