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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:

4ld2

1.550 Å

X-ray

2013-06-24

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:13.448
Number of residues:26
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.619361.125

% Hydrophobic% Polar
45.7954.21
According to VolSite

Ligand :
4ld2_1 Structure
HET Code: CTN
Formula: C9H13N3O5
Molecular weight: 243.217 g/mol
DrugBank ID: DB02097
Buried Surface Area:53.93 %
Polar Surface area: 128.61 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
21.579832.465646.0637


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
C1'CE2PHE- 483.580Hydrophobic
O2ND2ASN- 662.79137.12H-Bond
(Protein Donor)
O2'ND2ASN- 663.05150.42H-Bond
(Protein Donor)
C5'CD1PHE- 1413.80Hydrophobic
O5'NASP- 1422.87145.77H-Bond
(Protein Donor)
N4OE1GLU- 1432.7138.5H-Bond
(Ligand Donor)
N3OHOH- 3012.9179.94H-Bond
(Protein Donor)