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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:

3x2e

2.850 Å

X-ray

2014-12-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Adenosylhomocysteinase
ID:SAHH_THEMA
AC:O51933
Organism:Thermotoga maritima
Reign:Bacteria
TaxID:243274
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A90 %
B10 %


Ligand binding site composition:

B-Factor:70.253
Number of residues:50
Including
Standard Amino Acids: 50
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.4951991.250

% Hydrophobic% Polar
37.2962.71
According to VolSite

Ligand :
3x2e_1 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:60.08 %
Polar Surface area: 342.9 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 6
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
2.7309120.101646.197


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
O1NND2ASN- 1753.11134.08H-Bond
(Protein Donor)
C4NCG2THR- 1794.040Hydrophobic
O2NNCYS- 2083.11157.67H-Bond
(Protein Donor)
C5DCBCYS- 2084.250Hydrophobic
C1DSGCYS- 2084.290Hydrophobic
C4NSGCYS- 2084.320Hydrophobic
O3BOE2GLU- 2273.17159.96H-Bond
(Ligand Donor)
O2BOE1GLU- 2272.71154.7H-Bond
(Ligand Donor)
O2BNASP- 2293.48125.81H-Bond
(Protein Donor)
C1BCBSER- 2604.030Hydrophobic
N7NOALA- 2832.99149.7H-Bond
(Ligand Donor)
O7NND2ASN- 3303.49146.97H-Bond
(Protein Donor)
N7NOD1ASN- 3303.19157.72H-Bond
(Ligand Donor)
O7NNE2HIS- 3373.11130.22H-Bond
(Protein Donor)