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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:

4pzk

1.500 Å

X-ray

2014-03-31

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative tRNA (cytidine(34)-2'-O)-methyltransferase
ID:Q81YT5_BACAN
AC:Q81YT5
Organism:Bacillus anthracis
Reign:Bacteria
TaxID:1392
EC Number:/


Chains:

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


Ligand binding site composition:

B-Factor:13.355
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.561388.125

% Hydrophobic% Polar
37.3962.61
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4pzkHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4pzk_1 Structure
HET Code: SAH
Formula: C14H20N6O5S
Molecular weight: 384.411 g/mol
DrugBank ID: DB01752
Buried Surface Area:72.54 %
Polar Surface area: 212.38 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
4.18385-12.5553-15.51
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4pzkRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
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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
C2'CBLEU- 794.370Hydrophobic
O2'OLEU- 792.65154.57H-Bond
(Ligand Donor)
ONZLYS- 813.580Ionic
(Protein Cationic)
OXTNZLYS- 813.60Ionic
(Protein Cationic)
C1'CD1PHE- 1034.370Hydrophobic
O3'NGLY- 1043.16120.46H-Bond
(Protein Donor)
O2'NGLY- 1043.06165.3H-Bond
(Protein Donor)
N6OILE- 1253.03153.83H-Bond
(Ligand Donor)
N1NILE- 1252.9152.07H-Bond
(Protein Donor)
CBCBSER- 1333.740Hydrophobic
SDCBSER- 1334.010Hydrophobic
N7NLEU- 1342.99154.94H-Bond
(Protein Donor)
C5'CBLEU- 1364.340Hydrophobic
C4'CD1LEU- 1363.920Hydrophobic
C1'CG2THR- 1394.070Hydrophobic
O3'OHOH- 4203.37160.35H-Bond
(Ligand Donor)