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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:

2vf3

2.200 Å

X-ray

2007-10-30

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
B100 %


Ligand binding site composition:

B-Factor:44.218
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.851786.375

% Hydrophobic% Polar
41.6358.37
According to VolSite

Ligand :
2vf3_2 Structure
HET Code: GVS
Formula: C17H22N4O6S
Molecular weight: 410.445 g/mol
DrugBank ID: -
Buried Surface Area:58.82 %
Polar Surface area: 148.76 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 3
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 10

Mass center Coordinates

XYZ
5.10096-26.091-33.8811


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
OAPND2ASN- 112.53150.78H-Bond
(Protein Donor)
CAFCD1LEU- 143.490Hydrophobic
CAUCE2TYR- 243.920Hydrophobic
NAAOHIS- 252.9160.64H-Bond
(Ligand Donor)
OANND1HIS- 253.28159.7H-Bond
(Protein Donor)
CAFCD1ILE- 274.380Hydrophobic
CAJCD1ILE- 274.310Hydrophobic
NAHOHTYR- 312.96158.33H-Bond
(Ligand Donor)
CAJCBALA- 1293.770Hydrophobic
CAICBASP- 1304.290Hydrophobic
NAAOLYS- 1452.95141.36H-Bond
(Ligand Donor)
CASCBTHR- 1714.440Hydrophobic
CAOCE1TYR- 1753.970Hydrophobic
CASCD1TYR- 1753.210Hydrophobic
CAECD1LEU- 2084.210Hydrophobic