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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:

2e0i

2.800 Å

X-ray

2006-10-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA photolyase
ID:F9VNB1_SULTO
AC:F9VNB1
Organism:Sulfolobus tokodaii
Reign:Archaea
TaxID:273063
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:21.290
Number of residues:48
Including
Standard Amino Acids: 47
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.599907.875

% Hydrophobic% Polar
48.7051.30
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2e0iHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2e0i_4 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:66.98 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
13.764626.5745-4.24691
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2e0iRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.com


Binding mode :
What is Poseview ?
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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
C3'CBARG- 84.380Hydrophobic
C2'CDARG- 94.240Hydrophobic
C3'CBARG- 94.230Hydrophobic
C4'CDARG- 94.350Hydrophobic
N3OILE- 342.71168.89H-Bond
(Ligand Donor)
O4NASP- 363166.52H-Bond
(Protein Donor)
O2ANE2GLN- 392.72161.23H-Bond
(Protein Donor)
O3'NE2GLN- 393.23174.54H-Bond
(Protein Donor)
C5BCGGLN- 393.70Hydrophobic
C6CBGLN- 394.030Hydrophobic
C6CD2LEU- 404.020Hydrophobic
O2BOD1ASN- 432.58162.04H-Bond
(Ligand Donor)
C2BCBTYR- 454.150Hydrophobic
DuArDuArTYR- 453.470Aromatic Face/Face
C7MCGLYS- 463.770Hydrophobic
C8MCBALA- 504.220Hydrophobic
C7MCG2VAL- 513.570Hydrophobic
C1'SDMET- 544.320Hydrophobic
C9ASDMET- 543.670Hydrophobic
O4'OD2ASP- 982.82167.69H-Bond
(Ligand Donor)
O1POG1THR- 1002.53162.81H-Bond
(Protein Donor)
C5BCGPHE- 1023.940Hydrophobic
C4BCD2PHE- 1023.790Hydrophobic
C5'CD1PHE- 1023.880Hydrophobic
O3'NH1ARG- 1063.36142.06H-Bond
(Protein Donor)
O4'NH2ARG- 1063.18142.31H-Bond
(Protein Donor)
O2'NZLYS- 2213.03147.9H-Bond
(Protein Donor)
C8MCZPHE- 2223.920Hydrophobic
C1'CE1PHE- 2224.270Hydrophobic
N6AOE1GLU- 3313149.19H-Bond
(Ligand Donor)
N7AOHTYR- 3412.61162.33H-Bond
(Protein Donor)
N6AOHTYR- 3412.95152.17H-Bond
(Ligand Donor)
C8MCD1TYR- 3414.230Hydrophobic
O2OHOH- 50402.75154.54H-Bond
(Protein Donor)