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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:

5d12

3.000 Å

X-ray

2015-08-03

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
A100 %


Ligand binding site composition:

B-Factor:39.821
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.086796.500

% Hydrophobic% Polar
47.8852.12
According to VolSite

Ligand :
5d12_1 Structure
HET Code: G97
Formula: C20H16N6O
Molecular weight: 356.381 g/mol
DrugBank ID: -
Buried Surface Area:42.76 %
Polar Surface area: 95.59 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-10.218438.9086-2.34448


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
CAMCBLEU- 2734.490Hydrophobic
C5CD2LEU- 2734.140Hydrophobic
CAFCBVAL- 2814.080Hydrophobic
CADCG2VAL- 2814.120Hydrophobic
CAWCG1VAL- 2813.90Hydrophobic
NASOGLU- 3393.42140.26H-Bond
(Ligand Donor)
NAROMET- 3412.78136.37H-Bond
(Ligand Donor)
NANNMET- 3412.7149.74H-Bond
(Protein Donor)
CAHCD1LEU- 3934.460Hydrophobic