Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2gqt

1.300 Å

X-ray

2006-04-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-N-acetylenolpyruvoylglucosamine reductase
ID:MURB_THET8
AC:Q5SJC8
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:13.341
Number of residues:55
Including
Standard Amino Acids: 53
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0001272.375

% Hydrophobic% Polar
29.9770.03
According to VolSite

Ligand :
2gqt_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:72.19 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-0.256868-1.13396-0.336981


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
C8MCBTHR- 154.180Hydrophobic
O2BOVAL- 432.65151.53H-Bond
(Ligand Donor)
O2ANGLY- 452.79132.1H-Bond
(Protein Donor)
O1PNASN- 462.94168.11H-Bond
(Protein Donor)
O2ANGLY- 472.84145H-Bond
(Protein Donor)
C2'CBSER- 484.140Hydrophobic
C8MCBSER- 483.90Hydrophobic
O2'OGSER- 482.69158H-Bond
(Ligand Donor)
O2PNSER- 482.87159.5H-Bond
(Protein Donor)
O2POGSER- 482.6176.64H-Bond
(Protein Donor)
O1ANASN- 492.83163.91H-Bond
(Protein Donor)
C5BCBASN- 494.350Hydrophobic
C5'CBASN- 494.120Hydrophobic
C2'CBASN- 494.020Hydrophobic
C5BCD2LEU- 504.210Hydrophobic
C3BCD2LEU- 504.130Hydrophobic
C3'CG2ILE- 1044.30Hydrophobic
C8CGPRO- 1053.510Hydrophobic
C4'CBALA- 1063.590Hydrophobic
O1PNGLN- 1072.91148.07H-Bond
(Protein Donor)
C4BCGLYS- 1134.170Hydrophobic
C1BCGLYS- 1133.710Hydrophobic
C4BCGMET- 1144.060Hydrophobic
C3'CBALA- 1164.330Hydrophobic
O2NGLY- 1173158.06H-Bond
(Protein Donor)
N3OGLY- 1172.72177.83H-Bond
(Ligand Donor)
N6AOVAL- 1612.93165.97H-Bond
(Ligand Donor)
N1ANVAL- 1612.9145.98H-Bond
(Protein Donor)
O4NH2ARG- 1873.16130.8H-Bond
(Protein Donor)
O4NH1ARG- 1872.88140.54H-Bond
(Protein Donor)
N5NH2ARG- 1872.92152.51H-Bond
(Protein Donor)
O3BOE2GLU- 2643.41132.05H-Bond
(Ligand Donor)
O3BOE1GLU- 2642.53170.25H-Bond
(Ligand Donor)
C2BCZ2TRP- 2664.330Hydrophobic