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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:

3rh7

3.000 Å

X-ray

2011-04-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q92ZM6_RHIME
AC:Q92ZM6
Organism:Rhizobium meliloti
Reign:Bacteria
TaxID:266834
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A95 %
B3 %
E3 %


Ligand binding site composition:

B-Factor:71.456
Number of residues:37
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.676479.250

% Hydrophobic% Polar
32.3967.61
According to VolSite

Ligand :
3rh7_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:69.91 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
60.18511.2845100.754


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
C5'CBPHE- 373.450Hydrophobic
O2'OTHR- 382.86172.88H-Bond
(Ligand Donor)
C8CG2THR- 383.920Hydrophobic
N5NASN- 403.19151.69H-Bond
(Protein Donor)
C6CBASN- 403.610Hydrophobic
O4NSER- 413.32146.48H-Bond
(Protein Donor)
N3OCYS- 552.77151.88H-Bond
(Ligand Donor)
O2NALA- 572.83161.99H-Bond
(Protein Donor)
O3PNARG- 612.88174.88H-Bond
(Protein Donor)
O1PNASN- 623.47157.98H-Bond
(Protein Donor)
O3'OALA- 892.66175.63H-Bond
(Ligand Donor)
C2'CBALA- 894.440Hydrophobic
C9CBALA- 893.80Hydrophobic
O5'NH2ARG- 953.21154.89H-Bond
(Protein Donor)
O5'NH1ARG- 953.36145.92H-Bond
(Protein Donor)
C7MCGTYR- 1513.720Hydrophobic
C8CD1ILE- 2864.490Hydrophobic
C8MCBILE- 2863.960Hydrophobic