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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:

5fa5

2.340 Å

X-ray

2015-12-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein arginine N-methyltransferase 5
ID:ANM5_HUMAN
AC:O14744
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %
C0 %


Ligand binding site composition:

B-Factor:51.098
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.690340.875

% Hydrophobic% Polar
59.4140.59
According to VolSite

Ligand :
5fa5_1 Structure
HET Code: MTA
Formula: C11H15N5O3S
Molecular weight: 297.333 g/mol
DrugBank ID: DB02282
Buried Surface Area:77.92 %
Polar Surface area: 144.61 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-16.5497-101.011-3.908


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
S5'CGPRO- 3144.230Hydrophobic
C5'CBPRO- 31440Hydrophobic
C2'CBPRO- 3143.910Hydrophobic
S5'CD1LEU- 3194.10Hydrophobic
C3'CD1LEU- 3194.450Hydrophobic
C3'CE1TYR- 32440Hydrophobic
O3'OHTYR- 3242.65152.82H-Bond
(Protein Donor)
S5'CE2PHE- 3273.550Hydrophobic
O2'OE2GLU- 3922.64162.55H-Bond
(Ligand Donor)
O3'OE1GLU- 3922.62161.39H-Bond
(Ligand Donor)
O3'OE2GLU- 3923.26120.66H-Bond
(Ligand Donor)
N3NLYS- 3933.41137.9H-Bond
(Protein Donor)
N6OD1ASP- 4192.99148.44H-Bond
(Ligand Donor)
N1NMET- 4202.92169.73H-Bond
(Protein Donor)
CSCGGLU- 4353.660Hydrophobic
C1'CD2LEU- 4364.410Hydrophobic
C5'CD2LEU- 4364.110Hydrophobic
O2'OHOH- 8382.69150.88H-Bond
(Protein Donor)