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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:

3fpb

2.550 Å

X-ray

2009-01-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
ID:AT2A1_RABIT
AC:P04191
Organism:Oryctolagus cuniculus
Reign:Eukaryota
TaxID:9986
EC Number:3.6.3.8


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:99.999
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.3382332.125

% Hydrophobic% Polar
48.3451.66
According to VolSite

Ligand :
3fpb_1 Structure
HET Code: CZA
Formula: C20H20N2O3
Molecular weight: 336.384 g/mol
DrugBank ID: DB07604
Buried Surface Area:69 %
Polar Surface area: 77.42 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 5
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
31.95711.52111.2989


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
C1CE1PHE- 574.020Hydrophobic
C14CD1LEU- 613.830Hydrophobic
C8CD1LEU- 613.430Hydrophobic
C1CG1VAL- 623.810Hydrophobic
C7CG1VAL- 623.60Hydrophobic
C10CG1VAL- 623.750Hydrophobic
C10CD2LEU- 654.380Hydrophobic
C1CD1LEU- 983.820Hydrophobic
C10CD1LEU- 984.290Hydrophobic
C1CBASN- 1013.960Hydrophobic
O3ND2ASN- 1012.88134.57H-Bond
(Protein Donor)
C1CBALA- 1023.530Hydrophobic
C11CG2ILE- 3073.690Hydrophobic
C8CG2ILE- 3074.380Hydrophobic
C11CBGLU- 3093.940Hydrophobic
C19CD1LEU- 3113.370Hydrophobic
C12CGPRO- 3123.990Hydrophobic
O2MG MG- 10002.40Metal Acceptor
O1MG MG- 10002.360Metal Acceptor