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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:

2q85

2.510 Å

X-ray

2007-06-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-N-acetylenolpyruvoylglucosamine reductase
ID:MURB_ECOLI
AC:P08373
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:1.3.1.98


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:20.011
Number of residues:26
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0531140.750

% Hydrophobic% Polar
41.7258.28
According to VolSite

Ligand :
2q85_1 Structure
HET Code: 973
Formula: C21H12ClO3
Molecular weight: 347.771 g/mol
DrugBank ID: DB07296
Buried Surface Area:53.62 %
Polar Surface area: 49.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 4
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
4.97284-8.7756810.6188


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
CL1CD2LEU- 2184.250Hydrophobic
C20CD2LEU- 2183.50Hydrophobic
C19CBSER- 2294.330Hydrophobic
O3ND2ASN- 2333.32154.56H-Bond
(Protein Donor)
C6CBPRO- 2523.640Hydrophobic
C6CE2TYR- 2543.250Hydrophobic
C2CDLYS- 2623.950Hydrophobic
C1CBALA- 2644.020Hydrophobic
C20CGGLN- 2884.170Hydrophobic
C21CD1LEU- 2903.450Hydrophobic
CL1CG2VAL- 2913.920Hydrophobic
C20CG2VAL- 2913.540Hydrophobic
CL1C6FAD- 4023.430Hydrophobic