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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:

2pmd

2.650 Å

X-ray

2007-04-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Translation initiation factor 2 subunit gamma
ID:IF2G_SULSO
AC:Q980A5
Organism:Sulfolobus solfataricus
Reign:Archaea
TaxID:273057
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:72.305
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.043695.250

% Hydrophobic% Polar
54.3745.63
According to VolSite

Ligand :
2pmd_1 Structure
HET Code: GNP
Formula: C10H13N6O13P3
Molecular weight: 518.164 g/mol
DrugBank ID: DB02082
Buried Surface Area:52.38 %
Polar Surface area: 338.36 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
24.18334.99434-3.45616


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
C5'SDMET- 454.30Hydrophobic
O1GNZLYS- 2253.580Ionic
(Protein Cationic)
O1BNZLYS- 2252.860Ionic
(Protein Cationic)
O1BNZLYS- 2252.86152.31H-Bond
(Protein Donor)
N2OGSER- 2783.25120.68H-Bond
(Ligand Donor)
N2OSER- 2783.32144.05H-Bond
(Ligand Donor)
O2'NH2ARG- 2802.68133.4H-Bond
(Protein Donor)
N3NEARG- 2803.41125.82H-Bond
(Protein Donor)
N2OALA- 2962.51141.05H-Bond
(Ligand Donor)
C1'CBALA- 2964.310Hydrophobic
O2GOHOH- 4212.63179.99H-Bond
(Protein Donor)