scPDB - 4nxu entry

Protein Data Bank Entry:

PDB ID : 4nxu

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	27.474
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.313	1326.375

% Hydrophobic	% Polar
46.56	53.44
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	51.88 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-5.46167	-31.3854	-8.21626

Binding mode :

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
N7	OG	SER- 187	2.99	148.55	H-Bond (Protein Donor)	false
N6	OG	SER- 187	3.31	156.57	H-Bond (Ligand Donor)	false
O1B	OG	SER- 189	2.67	153.33	H-Bond (Protein Donor)	false
O2A	N	SER- 189	3.04	154.86	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 201	2.84	154.81	H-Bond (Protein Donor)	false
C2'	CG	GLN- 203	3.97	0	Hydrophobic	false
C2'	CD2	LEU- 313	4.32	0	Hydrophobic	false
C2'	CD	LYS- 326	4.44	0	Hydrophobic	false
O1A	NE	ARG- 342	2.65	170.69	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 342	3.53	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 368	2.77	167.37	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 368	2.77	0	Ionic (Protein Cationic)	false
O2'	O	HOH- 674	2.99	165.68	H-Bond (Ligand Donor)	false