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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:

3r9n

1.750 Å

X-ray

2011-03-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cyclin-dependent kinase 2
ID:CDK2_HUMAN
AC:P24941
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.22


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:16.317
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.914918.000

% Hydrophobic% Polar
47.0652.94
According to VolSite

Ligand :
3r9n_1 Structure
HET Code: Z68
Formula: C16H18N4O3S
Molecular weight: 346.404 g/mol
DrugBank ID: -
Buried Surface Area:68.46 %
Polar Surface area: 142.07 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
92.428780.0799-47.7339


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
S1CD1ILE- 104.110Hydrophobic
C11CD1ILE- 104.20Hydrophobic
C3CG1VAL- 184.040Hydrophobic
O3NZLYS- 332.7151.28H-Bond
(Protein Donor)
DuArNZLYS- 333.91141.41Pi/Cation
N4OGLU- 812.94152.65H-Bond
(Ligand Donor)
C11CE2PHE- 824.160Hydrophobic
C16CZPHE- 823.650Hydrophobic
N2NLEU- 833.44176.07H-Bond
(Protein Donor)
C13CBASP- 864.140Hydrophobic
C14CDLYS- 893.910Hydrophobic
C1CGGLN- 1313.650Hydrophobic
C6CBASN- 1323.80Hydrophobic
S1CD1LEU- 1343.750Hydrophobic
C12CD1LEU- 1343.750Hydrophobic
C5CBALA- 1444.380Hydrophobic