scPDB - 3dzd entry

Protein Data Bank Entry:

PDB ID : 3dzd

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Transcriptional regulator (NtrC family)
ID:	O66551_AQUAE
AC:	O66551
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	7 %
B	93 %

Ligand binding site composition:

B-Factor:	42.611
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.278	627.750

% Hydrophobic	% Polar
43.55	56.45
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	62.36 %
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
-33.7352	2.32196	28.5641

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
N6	O	VAL- 133	2.92	143.02	H-Bond (Ligand Donor)	false
N1	N	VAL- 133	2.9	168.46	H-Bond (Protein Donor)	false
O2B	N	GLY- 163	3.06	150.02	H-Bond (Protein Donor)	false
O3B	N	GLY- 165	2.76	136.3	H-Bond (Protein Donor)	false
O3A	N	GLY- 165	3.35	146.7	H-Bond (Protein Donor)	false
O3B	N	LYS- 166	2.91	178.26	H-Bond (Protein Donor)	false
O1B	N	GLU- 167	3.25	162.81	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 168	3.61	0	Hydrophobic	false
C1'	CZ	PHE- 316	4.43	0	Hydrophobic	false
C1'	CG1	VAL- 348	4.02	0	Hydrophobic	false
C5'	CB	ARG- 349	4.12	0	Hydrophobic	false
C4'	CD	LYS- 352	4.25	0	Hydrophobic	false