scPDB - 3jyo entry

Protein Data Bank Entry:

PDB ID : 3jyo

Resolution :1.000 Å

Experimental Method : X-ray

Deposition Date : 2009-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinate/shikimate dehydrogenase (NAD(+))
ID:	AROE_CORGL
AC:	Q9X5C9
Organism:	Corynebacterium glutamicum
Reign:	Bacteria
TaxID:	196627
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.097
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.337	681.750

% Hydrophobic	% Polar
51.49	48.51
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	53.5 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.8817	58.3103	1.5417

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
O1N	N	VAL- 138	2.84	160.08	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 138	4.13	0	Hydrophobic	false
C5N	CG2	VAL- 138	3.8	0	Hydrophobic	false
O3B	OD1	ASP- 158	2.65	171.62	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 158	3.3	130.84	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 158	2.74	169.14	H-Bond (Ligand Donor)	false
N3A	N	LEU- 159	3.38	154.02	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 163	3.35	147.7	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 163	2.81	142.9	H-Bond (Protein Donor)	false
C1B	CG2	THR- 202	4.18	0	Hydrophobic	false
C2D	SD	MET- 206	4.12	0	Hydrophobic	false
C4D	CG2	VAL- 228	3.87	0	Hydrophobic	false
N7N	O	VAL- 228	2.91	169.18	H-Bond (Ligand Donor)	false
N7N	O	GLY- 251	3.17	141.66	H-Bond (Ligand Donor)	false
O1N	O	HOH- 543	2.79	167.17	H-Bond (Protein Donor)	false