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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:

3hu3

2.200 Å

X-ray

2009-06-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transitional endoplasmic reticulum ATPase
ID:TERA_HUMAN
AC:P55072
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.6.4.6


Chains:

Chain Name:Percentage of Residues
within binding site
A89 %
B11 %


Ligand binding site composition:

B-Factor:35.871
Number of residues:37
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.3662217.375

% Hydrophobic% Polar
40.4959.51
According to VolSite

Ligand :
3hu3_1 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:66.42 %
Polar Surface area: 329.24 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
21.444947.192-11.3318


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
N6OGLY- 2072.84144.55H-Bond
(Ligand Donor)
N1NGLY- 2072.87171.35H-Bond
(Protein Donor)
O3BNGLY- 2482.99155.41H-Bond
(Protein Donor)
O1BNGLY- 2502.81144.94H-Bond
(Protein Donor)
O3GNZLYS- 2512.93130.25H-Bond
(Protein Donor)
O1BNZLYS- 2512.97155.51H-Bond
(Protein Donor)
O1BNLYS- 2512.99160.25H-Bond
(Protein Donor)
O3GNZLYS- 2512.930Ionic
(Protein Cationic)
O1BNZLYS- 2512.970Ionic
(Protein Cationic)
O2BNTHR- 2522.93160.01H-Bond
(Protein Donor)
O1ANLEU- 2532.94174.78H-Bond
(Protein Donor)
C3'CD1LEU- 2534.480Hydrophobic
C2'CD2LEU- 2534.360Hydrophobic
O3GND2ASN- 3483.08144.6H-Bond
(Protein Donor)
C5'CD1PHE- 36040Hydrophobic
C4'CE1PHE- 3603.80Hydrophobic
O2'CE1HIS- 3842.62156.86Weak HBond LIG
O2'NE2HIS- 3842.9160.74H-Bond
(Ligand Donor)
C5'CBALA- 4094.130Hydrophobic
C1'CBALA- 4124.220Hydrophobic
O2GMG MG- 8012.120Metal Acceptor
O2BMG MG- 8012.020Metal Acceptor
O2GOHOH- 8943.05179.96H-Bond
(Protein Donor)