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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:

2m3z

Å

NMR

2013-01-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1N5
AC:P12497
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11698
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:0.000
Number of residues:16
Including
Standard Amino Acids: 15
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.186290.250

% Hydrophobic% Polar
58.1441.86
According to VolSite

Ligand :
2m3z_2 Structure
HET Code: 1HF
Formula: C16H10N4O6S2
Molecular weight: 418.404 g/mol
DrugBank ID: -
Buried Surface Area:44.1 %
Polar Surface area: 188.55 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-13.56594.5455731.6553


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
C2CBARG- 323.50Hydrophobic
N2OGLY- 352.87143.7H-Bond
(Ligand Donor)
ONTRP- 372.92158.45H-Bond
(Protein Donor)
SCZ3TRP- 374.390Hydrophobic
C5CZ2TRP- 373.40Hydrophobic
O4NE2GLN- 452.88145.75H-Bond
(Protein Donor)
C4CGGLN- 453.870Hydrophobic
ONMET- 463.35134.82H-Bond
(Protein Donor)
SCGMET- 463.520Hydrophobic
SCGLYS- 474.090Hydrophobic
O1NZLYS- 473.09141.5H-Bond
(Protein Donor)