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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:

3ggj

2.600 Å

X-ray

2009-02-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Hypoxanthine-guanine phosphoribosyltransferase
ID:HPRT_HUMAN
AC:P00492
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.4.2.8


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:21.691
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.916904.500

% Hydrophobic% Polar
42.5457.46
According to VolSite

Ligand :
3ggj_2 Structure
HET Code: 25H
Formula: C9H12N5O5P
Molecular weight: 301.196 g/mol
DrugBank ID: -
Buried Surface Area:61.71 %
Polar Surface area: 167.53 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 2
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
17.161714.135617.7902


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
CAJCG2ILE- 1354.410Hydrophobic
CAGCG2ILE- 1354.340Hydrophobic
OACNASP- 1373158.75H-Bond
(Protein Donor)
CAJCBASP- 1374.280Hydrophobic
OADOG1THR- 1383.14147.1H-Bond
(Protein Donor)
OADNTHR- 1383.09153.25H-Bond
(Protein Donor)
OACNGLY- 1392.74153.82H-Bond
(Protein Donor)
OAENTHR- 1413.04152.75H-Bond
(Protein Donor)
N1OVAL- 1872.65160H-Bond
(Ligand Donor)
N2OVAL- 1873.12132.29H-Bond
(Ligand Donor)
O6NVAL- 1873173.55H-Bond
(Protein Donor)
OACOHOH- 2192.79179.94H-Bond
(Protein Donor)