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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:

4nxv

2.300 Å

X-ray

2013-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitochondrial dynamics protein MID51
ID:MID51_HUMAN
AC:Q9NQG6
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:40.410
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2381350.000

% Hydrophobic% Polar
47.5052.50
According to VolSite

Ligand :
4nxv_4 Structure
HET Code: GDP
Formula: C10H12N5O11P2
Molecular weight: 440.177 g/mol
DrugBank ID: DB04315
Buried Surface Area:52.05 %
Polar Surface area: 276.39 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
0.08110716.54904-45.808


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
N2OGSER- 1872.93169.23H-Bond
(Ligand Donor)
O3BOGSER- 1893.14151.81H-Bond
(Protein Donor)
O2ANSER- 1892.96140.58H-Bond
(Protein Donor)
O2BNE2HIS- 2012.55164.99H-Bond
(Protein Donor)
N2OE1GLN- 2033.35163.57H-Bond
(Ligand Donor)
O1ACZARG- 3423.630Ionic
(Protein Cationic)
O1ANEARG- 3422.59154.2H-Bond
(Protein Donor)
O2ANEARG- 3423.48125.53H-Bond
(Protein Donor)
O3BNZLYS- 3683.08147.99H-Bond
(Protein Donor)
O3ANZLYS- 3683.16126.63H-Bond
(Protein Donor)
O3BNZLYS- 3683.080Ionic
(Protein Cationic)