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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:

2gd6

2.300 Å

X-ray

2006-03-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )
ID:O06543_MYCTU
AC:O06543
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A19 %
B81 %


Ligand binding site composition:

B-Factor:36.250
Number of residues:49
Including
Standard Amino Acids: 48
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.048833.625

% Hydrophobic% Polar
47.7752.23
According to VolSite

Ligand :
2gd6_2 Structure
HET Code: ACO
Formula: C23H34N7O17P3S
Molecular weight: 805.539 g/mol
DrugBank ID: -
Buried Surface Area:52.98 %
Polar Surface area: 429.68 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 20

Mass center Coordinates

XYZ
118.22447.237419.7158


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
S1PCG2ILE- 163.410Hydrophobic
CH3CG2ILE- 163.660Hydrophobic
N6AOALA- 592.75161.05H-Bond
(Ligand Donor)
N1ANLEU- 613.19146.85H-Bond
(Protein Donor)
O8ANZLYS- 623.49164.98H-Bond
(Protein Donor)
O8ANZLYS- 623.490Ionic
(Protein Cationic)
N8POGLY- 833.35142.44H-Bond
(Ligand Donor)
C5BCD2TYR- 844.360Hydrophobic
O2ANARG- 852.98151.84H-Bond
(Protein Donor)
O2ACZARG- 853.710Ionic
(Protein Cationic)
C5BCG1VAL- 884.460Hydrophobic
C2BCG1VAL- 883.470Hydrophobic
O9ACZARG- 913.340Ionic
(Protein Cationic)
C2BCD1LEU- 924.290Hydrophobic
CDPCBALA- 1244.050Hydrophobic
C2PCBHIS- 1264.070Hydrophobic
C6PCZTYR- 1304.270Hydrophobic
C6PCEMET- 1883.790Hydrophobic
CH3SDMET- 1984.120Hydrophobic
CDPCE2PHE- 2443.910Hydrophobic