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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:

4mcc

1.950 Å

X-ray

2013-08-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:tRNA (guanine-N(1)-)-methyltransferase
ID:TRMD_HAEIN
AC:P43912
Organism:Haemophilus influenzae
Reign:Bacteria
TaxID:71421
EC Number:2.1.1.228


Chains:

Chain Name:Percentage of Residues
within binding site
A89 %
B11 %


Ligand binding site composition:

B-Factor:30.482
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.134914.625

% Hydrophobic% Polar
46.4953.51
According to VolSite

Ligand :
4mcc_1 Structure
HET Code: 21X
Formula: C15H15N4O2S
Molecular weight: 315.370 g/mol
DrugBank ID: -
Buried Surface Area:66.6 %
Polar Surface area: 126.43 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
22.218542.6479-1.556


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
S15CBLEU- 873.970Hydrophobic
C4CGPRO- 893.90Hydrophobic
N8OE2GLU- 1162.73162.14H-Bond
(Ligand Donor)
N8OE2GLU- 1162.730Ionic
(Ligand Cationic)
N22NILE- 1333.2172.6H-Bond
(Protein Donor)
N20OTYR- 1362.71163.62H-Bond
(Ligand Donor)
C4CG1VAL- 13740Hydrophobic
O19NLEU- 1382.85154.19H-Bond
(Protein Donor)
S15CGPRO- 1443.540Hydrophobic
N8OD2ASP- 1773.840Ionic
(Ligand Cationic)