scPDB - 3etd entry

Protein Data Bank Entry:

PDB ID : 3etd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-10-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate dehydrogenase 1, mitochondrial
ID:	DHE3_BOVIN
AC:	P00366
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	1.4.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
F	100 %

Ligand binding site composition:

B-Factor:	58.752
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.922	897.750

% Hydrophobic	% Polar
35.71	64.29
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	61.33 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
19.5484	18.737	129.787

Binding mode :

What is Poseview ?

2D View
3D View

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
O1X	NZ	LYS- 134	3.57	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 134	3.4	0	Ionic (Protein Cationic)	false
O2X	NZ	LYS- 134	3.4	126.21	H-Bond (Protein Donor)	false
C5D	CG	MET- 169	4.05	0	Hydrophobic	false
O7N	NH2	ARG- 211	2.96	156.85	H-Bond (Protein Donor)	false
C5N	CG2	THR- 215	3.67	0	Hydrophobic	false
O3B	N	PHE- 252	3.37	150.81	H-Bond (Protein Donor)	false
O1A	N	ASN- 254	3.02	142.63	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 255	4.02	0	Hydrophobic	false
O3B	OE1	GLU- 275	2.82	129.22	H-Bond (Ligand Donor)	false
C3B	CG	GLU- 275	4.19	0	Hydrophobic	false
O3X	OG	SER- 276	3	149.95	H-Bond (Protein Donor)	false
C4D	CB	ALA- 348	4.22	0	Hydrophobic	false
O3D	N	ASN- 349	2.73	160.64	H-Bond (Protein Donor)	false
C2D	CB	ASN- 349	4.07	0	Hydrophobic	false
C5N	CB	ASN- 374	4.36	0	Hydrophobic	false
C3N	CA	GLU- 550	4.05	0	Hydrophobic	false
C4N	CB	GLU- 550	3.79	0	Hydrophobic	false
O5B	O	HOH- 555	3.28	162.82	H-Bond (Protein Donor)	false