Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3r1q

1.850 Å

X-ray

2011-03-11

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:29.383
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.985509.625

% Hydrophobic% Polar
48.3451.66
According to VolSite

Ligand :
3r1q_1 Structure
HET Code: X75
Formula: C13H10Cl2N4O3
Molecular weight: 341.149 g/mol
DrugBank ID: -
Buried Surface Area:50.63 %
Polar Surface area: 113.82 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-65.6655-46.2778-11.1717


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C13CG2ILE- 103.660Hydrophobic
C17CG2ILE- 103.510Hydrophobic
C08CG2ILE- 103.360Hydrophobic
C05CG1VAL- 184.280Hydrophobic
C09CG1VAL- 183.970Hydrophobic
CL21CG2VAL- 184.020Hydrophobic
C05CBALA- 313.650Hydrophobic
N02OGLU- 812.93159.39H-Bond
(Ligand Donor)
N01OLEU- 833.02124.65H-Bond
(Ligand Donor)
O18NLEU- 832.92169.97H-Bond
(Protein Donor)
C12CD2LEU- 1344.080Hydrophobic
C06CD1LEU- 1343.650Hydrophobic