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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:

2j4k

2.200 Å

X-ray

2006-09-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uridylate kinase
ID:PYRH_SULSO
AC:Q97ZE2
Organism:Sulfolobus solfataricus
Reign:Archaea
TaxID:273057
EC Number:2.7.4.22


Chains:

Chain Name:Percentage of Residues
within binding site
A6 %
E94 %


Ligand binding site composition:

B-Factor:23.434
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.177516.375

% Hydrophobic% Polar
39.2260.78
According to VolSite

Ligand :
2j4k_5 Structure
HET Code: U5P
Formula: C9H11N2O9P
Molecular weight: 322.165 g/mol
DrugBank ID: -
Buried Surface Area:66.32 %
Polar Surface area: 181.33 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 4

Mass center Coordinates

XYZ
31.1794-5.85229-12.0822


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
O2PNGLY- 432.75170.19H-Bond
(Protein Donor)
C5'CBALA- 474.330Hydrophobic
O2'OD1ASP- 652.71173.69H-Bond
(Ligand Donor)
C1'CG1ILE- 694.240Hydrophobic
O4NPHE- 1132.9166.65H-Bond
(Protein Donor)
N3OGLN- 1142.52166.15H-Bond
(Ligand Donor)
O4NGLN- 1143.21153.6H-Bond
(Protein Donor)
O4NE2GLN- 1172.65160.77H-Bond
(Protein Donor)
O1POG1THR- 1192.6173.3H-Bond
(Protein Donor)
O1PNTHR- 1192.75166.26H-Bond
(Protein Donor)