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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:

3qwj

1.750 Å

X-ray

2011-02-28

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:30.113
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9281002.375

% Hydrophobic% Polar
43.7756.23
According to VolSite

Ligand :
3qwj_1 Structure
HET Code: X6A
Formula: C12H11ClN6O3
Molecular weight: 322.707 g/mol
DrugBank ID: -
Buried Surface Area:61.84 %
Polar Surface area: 152.73 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-38.7506-81.8767-46.5356


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
N06OE2GLU- 83.39140.19H-Bond
(Ligand Donor)
C15CG2ILE- 103.990Hydrophobic
CL22CG2ILE- 103.520Hydrophobic
C09CD1ILE- 104.10Hydrophobic
C10CG2ILE- 103.450Hydrophobic
C07CG1VAL- 184.190Hydrophobic
C11CG1VAL- 183.990Hydrophobic
CL22CG2VAL- 184.070Hydrophobic
C07CBALA- 313.540Hydrophobic
O20NZLYS- 333.950Ionic
(Protein Cationic)
N02OGLU- 812.88160.44H-Bond
(Ligand Donor)
N01OLEU- 832.99131.89H-Bond
(Ligand Donor)
O19NLEU- 832.96170.89H-Bond
(Protein Donor)
C14CD2LEU- 1343.980Hydrophobic
C08CD1LEU- 1343.680Hydrophobic