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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:

3ucb

1.380 Å

X-ray

2011-10-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV1BR
AC:P03367
Organism:Human immunodeficiency virus type 1 group M subtype B
Reign:Viruses
TaxID:11686
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A50 %
B50 %


Ligand binding site composition:

B-Factor:21.350
Number of residues:43
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.090681.750

% Hydrophobic% Polar
44.5555.45
According to VolSite

Ligand :
3ucb_1 Structure
HET Code: 017
Formula: C27H37N3O7S
Molecular weight: 547.664 g/mol
DrugBank ID: DB01264
Buried Surface Area:68.34 %
Polar Surface area: 148.79 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 12

Mass center Coordinates

XYZ
11.7861-7.88129-9.02918


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
C15CD2LEU- 233.720Hydrophobic
C33CD2LEU- 234.240Hydrophobic
O18OD2ASP- 252.65153.41H-Bond
(Ligand Donor)
O18OD1ASP- 252.67127.05H-Bond
(Ligand Donor)
O18OD1ASP- 252.76152.55H-Bond
(Protein Donor)
N20OGLY- 273.22161.7H-Bond
(Ligand Donor)
C16CBALA- 284.30Hydrophobic
C25CBALA- 284.060Hydrophobic
C4CBALA- 283.340Hydrophobic
O26NASP- 293.24124.02H-Bond
(Protein Donor)
O28NASP- 292.9164.24H-Bond
(Protein Donor)
C27CBASP- 294.050Hydrophobic
C29CBASP- 294.360Hydrophobic
N1OASN- 303.08155.65H-Bond
(Ligand Donor)
O26NASN- 303.39157.46H-Bond
(Protein Donor)
O26ND2ASN- 303.34120.75H-Bond
(Protein Donor)
C25CD1ILE- 323.650Hydrophobic
C3CD1ILE- 323.440Hydrophobic
C2CG1VAL- 474.390Hydrophobic
C7CBVAL- 473.960Hydrophobic
C14CG1ILE- 504.460Hydrophobic
C37CBILE- 504.370Hydrophobic
C24CD1ILE- 503.910Hydrophobic
C5CD1ILE- 503.620Hydrophobic
C36CGPRO- 813.520Hydrophobic
C15CG1VAL- 823.640Hydrophobic
C34CG1VAL- 823.60Hydrophobic
C32CG1VAL- 844.450Hydrophobic
C3CG2VAL- 843.960Hydrophobic
N1OHOH- 10453.07162.62H-Bond
(Ligand Donor)