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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:

3lij

1.900 Å

X-ray

2010-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
ID:Q5CS01_CRYPI
AC:Q5CS01
Organism:Cryptosporidium parvum
Reign:Eukaryota
TaxID:353152
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:45.393
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.304840.375

% Hydrophobic% Polar
56.6343.37
According to VolSite

Ligand :
3lij_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:49.58 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-0.2615169.0494227.1042


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'CD2LEU- 684.220Hydrophobic
C1'CG1VAL- 764.290Hydrophobic
C5'CG2VAL- 763.780Hydrophobic
O2ANZLYS- 913.510Ionic
(Protein Cationic)
N6OGLU- 1392.95160.1H-Bond
(Ligand Donor)
N1NTYR- 1412.95175.32H-Bond
(Protein Donor)
O2'OE2GLU- 1453.43162.63H-Bond
(Ligand Donor)
O1GMG MG- 5212.530Metal Acceptor