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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:

3lut

2.900 Å

X-ray

2010-02-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Voltage-gated potassium channel subunit beta-2
ID:KCAB2_RAT
AC:P62483
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:60.053
Number of residues:59
Including
Standard Amino Acids: 55
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.202715.500

% Hydrophobic% Polar
40.5759.43
According to VolSite

Ligand :
3lut_1 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:80.98 %
Polar Surface area: 405.54 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
75.5588106.30911.2172


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
O3DNTRP- 573.1151.79H-Bond
(Protein Donor)
C3DCBTRP- 573.460Hydrophobic
O3XNE2GLN- 632.88168.84H-Bond
(Protein Donor)
O2DOD1ASP- 852.97167.88H-Bond
(Ligand Donor)
C2DCE2TYR- 904.030Hydrophobic
O7NND2ASN- 1583.48128.13H-Bond
(Protein Donor)
N7NOGSER- 1882.8162.61H-Bond
(Ligand Donor)
O7NNEARG- 1892.72139.89H-Bond
(Protein Donor)
O7NNH2ARG- 1892.59144.49H-Bond
(Protein Donor)
N7NOE1GLN- 2142.79142.83H-Bond
(Ligand Donor)
C4NCE3TRP- 2433.160Hydrophobic
C5DCBTRP- 2434.280Hydrophobic
C3NCBTRP- 2434.080Hydrophobic
O1ANLEU- 2463.17132.15H-Bond
(Protein Donor)
O2ANLEU- 2463.14143.97H-Bond
(Protein Donor)
O1ANCYS- 2482.75145.9H-Bond
(Protein Donor)
N3ANZLYS- 2543.1132.52H-Bond
(Protein Donor)
O1XNZLYS- 2543160.67H-Bond
(Protein Donor)
O2XNZLYS- 2543.01122.58H-Bond
(Protein Donor)
O1XNZLYS- 25430Ionic
(Protein Cationic)
O2XNZLYS- 2543.010Ionic
(Protein Cationic)
O3BNH2ARG- 2642.76120.31H-Bond
(Protein Donor)
O1NNH1ARG- 2642.63143.09H-Bond
(Protein Donor)
O1NNH2ARG- 2642.72138.49H-Bond
(Protein Donor)
O1NCZARG- 2643.080Ionic
(Protein Cationic)
C4DCBLEU- 3213.90Hydrophobic
C2BCBSER- 3254.360Hydrophobic
O2BOGSER- 3253.05147.11H-Bond
(Protein Donor)
O2XOGSER- 3253.08143.03H-Bond
(Protein Donor)
O2BNE2GLN- 3293.49135.11H-Bond
(Protein Donor)
O2XNE2GLN- 3293.29164.85H-Bond
(Protein Donor)
N6AOE1GLU- 3323.23146.73H-Bond
(Ligand Donor)
N7AND2ASN- 3333.07140.12H-Bond
(Protein Donor)
N6AOD1ASN- 3332.96136.14H-Bond
(Ligand Donor)
O2AOHOH- 3952.78179.97H-Bond
(Protein Donor)
O3XOHOH- 4103179.96H-Bond
(Protein Donor)
O3DOHOH- 4352.98164.94H-Bond
(Ligand Donor)