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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:

3keo

1.500 Å

X-ray

2009-10-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Redox-sensing transcriptional repressor Rex
ID:REX_STRA3
AC:Q8E565
Organism:Streptococcus agalactiae serotype III
Reign:Bacteria
TaxID:211110
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A75 %
B25 %


Ligand binding site composition:

B-Factor:15.252
Number of residues:42
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.488317.250

% Hydrophobic% Polar
40.4359.57
According to VolSite

Ligand :
3keo_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:65.75 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
35.635956.736745.8001


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
O2ANASN- 943.06168.91H-Bond
(Protein Donor)
O1NND2ASN- 942.88170.85H-Bond
(Protein Donor)
O2NNILE- 952.99157.83H-Bond
(Protein Donor)
C3NCBILE- 954.010Hydrophobic
C5DCG2ILE- 954.010Hydrophobic
N7NOALA- 982.98139.75H-Bond
(Ligand Donor)
C4NCD2LEU- 994.10Hydrophobic
C2DCE1TYR- 10240Hydrophobic
C3NCBTYR- 1023.820Hydrophobic
DuArDuArTYR- 1023.730Aromatic Face/Face
O3BOD1ASP- 1172.8169.68H-Bond
(Ligand Donor)
O2BOD2ASP- 1172.58172.64H-Bond
(Ligand Donor)
C2BCD1LEU- 1184.450Hydrophobic
C5BCGPRO- 1573.780Hydrophobic
O3DOGSER- 1582.82159.3H-Bond
(Ligand Donor)
O3DOGSER- 1802.74164.87H-Bond
(Protein Donor)
C5NCD1LEU- 1973.630Hydrophobic
O2NOHOH- 2252.74167.37H-Bond
(Protein Donor)