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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:

3of1

2.210 Å

X-ray

2010-08-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-dependent protein kinase regulatory subunit
ID:KAPR_YEAST
AC:P07278
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:48.929
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.669543.375

% Hydrophobic% Polar
56.5243.48
According to VolSite

Ligand :
3of1_1 Structure
HET Code: CMP
Formula: C10H11N5O6P
Molecular weight: 328.198 g/mol
DrugBank ID: DB02527
Buried Surface Area:74.95 %
Polar Surface area: 167.48 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 2
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-53.676918.0845-27.5375


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
C5'CD1ILE- 2123.320Hydrophobic
C4'CE1PHE- 2314.480Hydrophobic
C1'CE1PHE- 2313.650Hydrophobic
N7ND2ASN- 2393.1145.25H-Bond
(Protein Donor)
C4'CBPHE- 2474.470Hydrophobic
C1'CBPHE- 2474.180Hydrophobic
O1POGLY- 2483.43132.2H-Bond
(Ligand Donor)
O2'NGLY- 2483.08130.36H-Bond
(Protein Donor)
C3'CD1LEU- 2503.70Hydrophobic
O1PNALA- 2512.94158.63H-Bond
(Protein Donor)
O1PNH1ARG- 2582.6147.25H-Bond
(Protein Donor)
O2PNALA- 2592.89167.09H-Bond
(Protein Donor)
C5'CBALA- 2604.010Hydrophobic
C5'CG2VAL- 2624.020Hydrophobic