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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:

2v2v

2.400 Å

X-ray

2007-06-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
ID:ISPE_AQUAE
AC:O67060
Organism:Aquifex aeolicus
Reign:Bacteria
TaxID:224324
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:39.968
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.754698.625

% Hydrophobic% Polar
40.1059.90
According to VolSite

Ligand :
2v2v_1 Structure
HET Code: V12
Formula: C18H20N6O5
Molecular weight: 400.389 g/mol
DrugBank ID: -
Buried Surface Area:44.74 %
Polar Surface area: 166.16 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 5
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
16.1204-10.780520.1011


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
CBACE2TYR- 2440Hydrophobic
CAZCZTYR- 243.740Hydrophobic
OACND1HIS- 252.83169.14H-Bond
(Protein Donor)
NAONHIS- 253.15149.68H-Bond
(Protein Donor)
NAAOHIS- 253.04160.21H-Bond
(Ligand Donor)
NAAOLYS- 1453.19163.82H-Bond
(Ligand Donor)
CAHCBSER- 1703.740Hydrophobic
CB0CG2THR- 1714.410Hydrophobic
CALCBTHR- 1713.620Hydrophobic
CBCCD1TYR- 1753.530Hydrophobic