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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:

3r0y

1.650 Å

X-ray

2011-03-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pol protein
ID:Q000H7_9HIV1
AC:Q000H7
Organism:Human immunodeficiency virus 1
Reign:Viruses
TaxID:11676
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A44 %
B56 %


Ligand binding site composition:

B-Factor:22.339
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.295384.750

% Hydrophobic% Polar
39.4760.53
According to VolSite

Ligand :
3r0y_1 Structure
HET Code: RSZ
Formula: C34H39N5O5
Molecular weight: 597.704 g/mol
DrugBank ID: -
Buried Surface Area:38.66 %
Polar Surface area: 149.51 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 5
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 15

Mass center Coordinates

XYZ
14.12389.32434-0.0489773


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
O42ND2ASN- 253.11149.41H-Bond
(Protein Donor)
O42ND2ASN- 252.99148.24H-Bond
(Protein Donor)
O43ND2ASN- 252.84126.09H-Bond
(Protein Donor)
C39CBILE- 473.890Hydrophobic
C08CBILE- 504.40Hydrophobic
C09CG1ILE- 503.680Hydrophobic
C18CGPRO- 813.710Hydrophobic
C36CGPRO- 813.740Hydrophobic
C30CBTHR- 824.20Hydrophobic
C29CG2THR- 823.740Hydrophobic
C19CBTHR- 823.650Hydrophobic
C18CG2VAL- 844.210Hydrophobic
C19CG2VAL- 844.440Hydrophobic
C30CG2VAL- 843.370Hydrophobic