Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2zev

2.230 Å

X-ray

2007-12-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Geranylgeranyl pyrophosphate synthase
ID:GGPPS_YEAST
AC:Q12051
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:42.440
Number of residues:38
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
1.053580.500

% Hydrophobic% Polar
61.6338.37
According to VolSite

Ligand :
2zev_1 Structure
HET Code: B71
Formula: C17H28NO7P2
Molecular weight: 420.354 g/mol
DrugBank ID: -
Buried Surface Area:61.21 %
Polar Surface area: 159.1 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 0
Rings: 1
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 14

Mass center Coordinates

XYZ
30.966448.29988.53081


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CAMCGARG- 443.990Hydrophobic
CAACD2LEU- 473.730Hydrophobic
CAACG1ILE- 484.020Hydrophobic
CAMCG1VAL- 693.560Hydrophobic
OAFNH2ARG- 892.85136.01H-Bond
(Protein Donor)
OACNH2ARG- 893.43127.39H-Bond
(Protein Donor)
OACNH1ARG- 892.65169H-Bond
(Protein Donor)
OAFCZARG- 893.690Ionic
(Protein Cationic)
OACCZARG- 893.490Ionic
(Protein Cationic)
CAICD1LEU- 1433.60Hydrophobic
OABNZLYS- 1743.06159.91H-Bond
(Protein Donor)
OABNZLYS- 1743.060Ionic
(Protein Cationic)
CAHCGLYS- 1743.570Hydrophobic
CATCG2THR- 1753.60Hydrophobic
CALCD1PHE- 1794.250Hydrophobic
CAQCZPHE- 1793.270Hydrophobic
CARCE2PHE- 1793.990Hydrophobic
CAACG2THR- 1823.440Hydrophobic
CALCBTHR- 1824.130Hydrophobic
CAQCZTYR- 2103.920Hydrophobic
CARCE2TYR- 2103.340Hydrophobic
OADNE2GLN- 2113.43142.85H-Bond
(Protein Donor)
OAGOD1ASP- 2142.82156.67H-Bond
(Protein Donor)
OADOD1ASP- 2143.03129.07H-Bond
(Protein Donor)
OAGNZLYS- 2383.920Ionic
(Protein Cationic)
OAENZLYS- 2383.350Ionic
(Protein Cationic)
OAENZLYS- 2383.35127.34H-Bond
(Protein Donor)
OAEMG MG- 13012.230Metal Acceptor
OAFMG MG- 13022.150Metal Acceptor
OAEMG MG- 13022.140Metal Acceptor