scPDB - 5ijz entry

Protein Data Bank Entry:

PDB ID : 5ijz

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2016-03-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADP-specific glutamate dehydrogenase
ID:	DHE4_CORGL
AC:	P31026
Organism:	Corynebacterium glutamicum
Reign:	Bacteria
TaxID:	196627
EC Number:	1.4.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	67.960
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.708	1782.000

% Hydrophobic	% Polar
33.52	66.48
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	53.1 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
8.14546	-0.51025	66.221

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
C5N	CD	LYS- 116	4.47	0	Hydrophobic	false
O2D	OD2	ASP- 168	3.27	157.97	H-Bond (Ligand Donor)	false
C5B	CG1	ILE- 169	4.06	0	Hydrophobic	false
C3D	CD1	ILE- 169	4.28	0	Hydrophobic	false
O7N	OG1	THR- 212	2.76	137.68	H-Bond (Protein Donor)	false
O1A	N	ASN- 243	3.1	164.03	H-Bond (Protein Donor)	false
N7N	OD1	ASN- 243	3.48	120.1	H-Bond (Ligand Donor)	false
O1N	N	VAL- 244	3.22	170.32	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 244	3.83	0	Hydrophobic	false
C5D	CG2	VAL- 244	3.78	0	Hydrophobic	false
C4B	CB	ALA- 321	4.28	0	Hydrophobic	false
C1B	CB	ALA- 321	3.76	0	Hydrophobic	false
O3D	O	ALA- 321	3.03	139.49	H-Bond (Ligand Donor)	false
O3D	N	ASN- 347	3.3	162.65	H-Bond (Protein Donor)	false
C2D	CB	ASN- 347	4.42	0	Hydrophobic	false
O1N	O	HOH- 635	2.95	179.94	H-Bond (Protein Donor)	false