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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:

1ne4

2.400 Å

X-ray

2002-12-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP-dependent protein kinase type I-alpha regulatory subunit
ID:KAP0_BOVIN
AC:P00514
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:72.491
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.331330.750

% Hydrophobic% Polar
73.4726.53
According to VolSite

Ligand :
1ne4_2 Structure
HET Code: RP1
Formula: C10H12N5O5PS
Molecular weight: 345.272 g/mol
DrugBank ID: DB01790
Buried Surface Area:76.43 %
Polar Surface area: 179.67 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
75.328647.054793.4119


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'CG1VAL- 2814.40Hydrophobic
C4'CBPHE- 3224.240Hydrophobic
C1'CBPHE- 3223.890Hydrophobic
O2'NGLY- 3232.95155.42H-Bond
(Protein Donor)
O2'OE2GLU- 3242.61148.67H-Bond
(Ligand Donor)
C3'CD1ILE- 3254.060Hydrophobic
C5'CBARG- 3334.470Hydrophobic
O2PNALA- 3342.55157.18H-Bond
(Protein Donor)
C5'CBALA- 3353.790Hydrophobic
C5'CG2VAL- 3374.210Hydrophobic
C2'CZTYR- 3714.030Hydrophobic
N6OASN- 3723.44132.15H-Bond
(Ligand Donor)