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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:

4hrq

1.900 Å

X-ray

2012-10-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cytidine and deoxycytidylate deaminase zinc-binding region
ID:Q82Y41_NITEU
AC:Q82Y41
Organism:Nitrosomonas europaea
Reign:Bacteria
TaxID:228410
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
B4 %


Ligand binding site composition:

B-Factor:15.696
Number of residues:29
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.612408.375

% Hydrophobic% Polar
44.6355.37
According to VolSite

Ligand :
4hrq_1 Structure
HET Code: AZG
Formula: C4H4N6O
Molecular weight: 152.114 g/mol
DrugBank ID: DB01667
Buried Surface Area:65.64 %
Polar Surface area: 113.6 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
23.459234.090446.3903


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
DuArDuArPHE- 483.880Aromatic Face/Face
N7ND2ASN- 662.65139.07H-Bond
(Protein Donor)
DuArDuArHIS- 773.790Aromatic Face/Face
N8NALA- 783161.08H-Bond
(Protein Donor)
N9OE1GLU- 792.94142.61H-Bond
(Ligand Donor)
N2OASP- 1423.23143.06H-Bond
(Ligand Donor)
N2OE1GLU- 1432.87148.39H-Bond
(Ligand Donor)
N3OHOH- 3032.7151.72H-Bond
(Protein Donor)