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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:

3dqw

2.020 Å

X-ray

2008-07-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Proto-oncogene tyrosine-protein kinase Src
ID:SRC_CHICK
AC:P00523
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:2.7.10.2


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:37.256
Number of residues:36
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.0981208.250

% Hydrophobic% Polar
49.7250.28
According to VolSite

Ligand :
3dqw_3 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:53.78 %
Polar Surface area: 329.24 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-23.053-3.2775514.9152


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
O1BMG MG- 32.60Metal Acceptor
C1'CBLEU- 2734.020Hydrophobic
C5'CG2VAL- 2814.240Hydrophobic
C1'CG1VAL- 2814.430Hydrophobic
O2ANZLYS- 2953.41154.39H-Bond
(Protein Donor)
O2ANZLYS- 2953.410Ionic
(Protein Cationic)
N6OGLU- 3392.76158.66H-Bond
(Ligand Donor)
N1NMET- 3412.9172.18H-Bond
(Protein Donor)
C3'CBSER- 3454.310Hydrophobic
O1AOD1ASP- 4043.44136.06H-Bond
(Protein Donor)
O2AOD1ASP- 4042.55153.65H-Bond
(Protein Donor)