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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:

2oo7

1.800 Å

X-ray

2007-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Adenylate kinase
ID:KAD_BACSU
AC:P16304
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:12.945
Number of residues:63
Including
Standard Amino Acids: 60
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.051469.125

% Hydrophobic% Polar
46.7653.24
According to VolSite

Ligand :
2oo7_1 Structure
HET Code: AP5
Formula: C20H24N10O22P5
Molecular weight: 911.327 g/mol
DrugBank ID: DB01717
Buried Surface Area:78.76 %
Polar Surface area: 543.69 Å2
Number of
H-Bond Acceptors: 30
H-Bond Donors: 6
Rings: 6
Aromatic rings: 4
Anionic atoms: 5
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 16

Mass center Coordinates

XYZ
37.344960.750144.4826


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
O3BNGLY- 103.35136.78H-Bond
(Protein Donor)
O1BNGLY- 123.04151.01H-Bond
(Protein Donor)
O1BNLYS- 132.87151.37H-Bond
(Protein Donor)
O1DNZLYS- 133.03173.88H-Bond
(Protein Donor)
O1DNZLYS- 133.030Ionic
(Protein Cationic)
O2BNGLY- 142.77157.79H-Bond
(Protein Donor)
O1ANTHR- 152.82144.53H-Bond
(Protein Donor)
O1AOG1THR- 152.7163.51H-Bond
(Protein Donor)
N7BOG1THR- 312.84167.91H-Bond
(Protein Donor)
C1JCD1PHE- 354.030Hydrophobic
O1ECZARG- 363.650Ionic
(Protein Cationic)
O1ENH1ARG- 363.1151.09H-Bond
(Protein Donor)
O1ENH2ARG- 363.33139.76H-Bond
(Protein Donor)
C4JCG1ILE- 534.080Hydrophobic
C1JCG1ILE- 533.870Hydrophobic
O2JOGLU- 572.61155.79H-Bond
(Ligand Donor)
C1JCG2VAL- 594.230Hydrophobic
N3BNVAL- 593.05152.42H-Bond
(Protein Donor)
N6BOGLY- 852.9131.84H-Bond
(Ligand Donor)
O1DNH2ARG- 883.12142.13H-Bond
(Protein Donor)
O1DNH1ARG- 882.93153.43H-Bond
(Protein Donor)
O2ENH2ARG- 882.96125.66H-Bond
(Protein Donor)
N7BNEARG- 883.31120.73H-Bond
(Protein Donor)
O1DCZARG- 883.470Ionic
(Protein Cationic)
N6BOE1GLN- 922.91173.83H-Bond
(Ligand Donor)
N1BNE2GLN- 923.04157.69H-Bond
(Protein Donor)
C4FCBARG- 1234.310Hydrophobic
DuArCZARG- 1233.647.65Pi/Cation
C5FCD2LEU- 1244.330Hydrophobic
O2ACZARG- 1273.930Ionic
(Protein Cationic)
O1GCZARG- 1273.380Ionic
(Protein Cationic)
O2GCZARG- 1273.80Ionic
(Protein Cationic)
O2ANH2ARG- 1272.86142.25H-Bond
(Protein Donor)
O1GNH1ARG- 1272.87123.16H-Bond
(Protein Donor)
O2GNH2ARG- 1272.94170.39H-Bond
(Protein Donor)
C3FCDARG- 1273.690Hydrophobic
O2AOG1THR- 1363.42153.78H-Bond
(Protein Donor)
C3FCBTHR- 1364.170Hydrophobic
O3FOTYR- 1372.73152.34H-Bond
(Ligand Donor)
C1FCBHIS- 1384.280Hydrophobic
O1GCZARG- 1603.820Ionic
(Protein Cationic)
O2GCZARG- 1603.980Ionic
(Protein Cationic)
O1ECZARG- 1603.640Ionic
(Protein Cationic)
O2GNH2ARG- 1603.09143.53H-Bond
(Protein Donor)
O1ENH2ARG- 1603.14123.07H-Bond
(Protein Donor)
O2DCZARG- 1713.780Ionic
(Protein Cationic)
O2DNH1ARG- 1712.84162.58H-Bond
(Protein Donor)
N6AOARG- 1992.85175.12H-Bond
(Ligand Donor)
O2BMG MG- 9232.510Metal Acceptor
O2GMG MG- 9232.550Metal Acceptor
O3JOHOH- 12282.79179.96H-Bond
(Protein Donor)