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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:

4rh1

2.600 Å

X-ray

2014-10-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Spore photoproduct lyase
ID:A4IQU1_GEOTN
AC:A4IQU1
Organism:Geobacillus thermodenitrificans
Reign:Bacteria
TaxID:420246
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:40.100
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.202847.125

% Hydrophobic% Polar
48.2151.79
According to VolSite

Ligand :
4rh1_1 Structure
HET Code: 0TT
Formula: C20H28N4O10
Molecular weight: 484.457 g/mol
DrugBank ID: -
Buried Surface Area:57.72 %
Polar Surface area: 198.19 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 6
Rings: 4
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-20.8576-1.3689123.5228


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
CHSGCYS- 764.120Hydrophobic
N2OLYS- 772.73157.37H-Bond
(Ligand Donor)
O4NSER- 793.3142.11H-Bond
(Protein Donor)
C8CD1TYR- 983.320Hydrophobic
CACE1TYR- 983.650Hydrophobic
O1OG1THR- 1023.16156.21H-Bond
(Ligand Donor)
CHCGGLU- 1374.280Hydrophobic
CHCBALA- 1404.270Hydrophobic
C1CG1VAL- 1723.640Hydrophobic
O6NH1ARG- 1933.25174.08H-Bond
(Protein Donor)
C3CG2ILE- 2703.680Hydrophobic
C4CDARG- 2733.930Hydrophobic
N4OHTYR- 3392.75169.22H-Bond
(Ligand Donor)