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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:

2zsd

2.500 Å

X-ray

2008-09-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pantothenate kinase
ID:COAA_MYCTU
AC:P9WPA7
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:2.7.1.33


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:43.559
Number of residues:47
Including
Standard Amino Acids: 46
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9471080.000

% Hydrophobic% Polar
49.0650.94
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2zsdHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2zsd_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:61.95 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
45.067136.405529.2733
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2zsdRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.com


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
CAPCG2VAL- 994.130Hydrophobic
O1ANALA- 1002.56151.72H-Bond
(Protein Donor)
O2ANZLYS- 1032.91148.62H-Bond
(Protein Donor)
O4ANZLYS- 1032.53136.68H-Bond
(Protein Donor)
O2ANZLYS- 1032.910Ionic
(Protein Cationic)
O4ANZLYS- 1032.530Ionic
(Protein Cationic)
O7AOGSER- 1042.8159.28H-Bond
(Protein Donor)
O8AOGSER- 1043.16126.76H-Bond
(Protein Donor)
C5BCBSER- 1044.420Hydrophobic
O7ACZARG- 1083.490Ionic
(Protein Cationic)
O9ACZARG- 1083.930Ionic
(Protein Cationic)
O7ANH1ARG- 1082.63159.76H-Bond
(Protein Donor)
O8ANH2ARG- 1083.37162.79H-Bond
(Protein Donor)
O5AOD2ASP- 1293.16163.72H-Bond
(Protein Donor)
CDPCD1LEU- 1324.370Hydrophobic
CEPCD1LEU- 1324.480Hydrophobic
CDPCGLYS- 1474.490Hydrophobic
CEPCZTYR- 1774.050Hydrophobic
O5ANE2HIS- 1793.16156.96H-Bond
(Protein Donor)
CEPCE1TYR- 1824.290Hydrophobic
C6PCZTYR- 1824.320Hydrophobic
CDPCD1LEU- 2034.110Hydrophobic
O1ANH1ARG- 2383.38136.4H-Bond
(Protein Donor)
O1ANH2ARG- 2382.92164.53H-Bond
(Protein Donor)
O1ACZARG- 2383.590Ionic
(Protein Cationic)
S1PCE1PHE- 2393.880Hydrophobic
C1BCEMET- 2424.380Hydrophobic
S1PCZPHE- 2473.60Hydrophobic
C2PCZPHE- 2543.240Hydrophobic
S1PCE2PHE- 2543.930Hydrophobic
S1PCE1TYR- 2574.370Hydrophobic
C6PCG2ILE- 2764.350Hydrophobic
O5PND2ASN- 2773.39154.24H-Bond
(Protein Donor)
O5AOHOH- 4453.35179.98H-Bond
(Protein Donor)