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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:

2y65

2.200 Å

X-ray

2011-01-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Kinesin heavy chain
ID:KINH_DROME
AC:P17210
Organism:Drosophila melanogaster
Reign:Eukaryota
TaxID:7227
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A16 %
B84 %


Ligand binding site composition:

B-Factor:29.417
Number of residues:33
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.1921120.500

% Hydrophobic% Polar
42.4757.53
According to VolSite

Ligand :
2y65_2 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:55.97 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
24.390923.0321-43.2473


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
O1BNSER- 952.62153.66H-Bond
(Protein Donor)
C5'CBSER- 954.50Hydrophobic
O3BNGLY- 973.09155.68H-Bond
(Protein Donor)
O3ANGLY- 973.28128.63H-Bond
(Protein Donor)
O1BNZLYS- 983.970Ionic
(Protein Cationic)
O3BNZLYS- 982.960Ionic
(Protein Cationic)
O3BNZLYS- 982.96175.85H-Bond
(Protein Donor)
O3BNLYS- 982.93144.24H-Bond
(Protein Donor)
O2BNTHR- 992.96159.83H-Bond
(Protein Donor)
O2ANHIS- 1002.59161.48H-Bond
(Protein Donor)
C2'CBHIS- 1004.250Hydrophobic
O2BMG MG- 8002.080Metal Acceptor