scPDB - 3pjt entry

Protein Data Bank Entry:

PDB ID : 3pjt

Resolution :2.520 Å

Experimental Method : X-ray

Deposition Date : 2010-11-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diguanylate cyclase/phosphodiesterase
ID:	Q3KK31_PSEPF
AC:	Q3KK31
Organism:	Pseudomonas fluorescens
Reign:	Bacteria
TaxID:	205922
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.095
Number of residues:	47
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.198	732.375

% Hydrophobic	% Polar
39.63	60.37
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	67.54 %
Polar Surface area:	366.32 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	6
Rings:	7
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-20.1088	-45.1321	13.6061

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
O1P	O	HOH- 2	2.76	171.46	H-Bond (Protein Donor)	false
N11	O	HOH- 18	2.68	146.54	H-Bond (Ligand Donor)	false
O2'	O	HOH- 35	3.12	175.88	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 431	3.33	142.78	H-Bond (Protein Donor)	false
C3'	CG	LEU- 448	4.38	0	Hydrophobic	false
C5A	CD1	LEU- 448	4.17	0	Hydrophobic	false
C3A	CD1	LEU- 448	4.2	0	Hydrophobic	false
N71	N	SER- 449	3.01	158.22	H-Bond (Protein Donor)	false
O21	NH2	ARG- 450	2.78	138.67	H-Bond (Protein Donor)	false
C5A	CB	ALA- 461	3.87	0	Hydrophobic	false
C1A	CB	ALA- 461	4.47	0	Hydrophobic	false
O11	N	GLY- 462	2.89	156.61	H-Bond (Protein Donor)	false
C1A	CD1	LEU- 465	3.74	0	Hydrophobic	false
N21	OD1	ASP- 478	3.16	169.62	H-Bond (Ligand Donor)	false
O1P	NE2	GLN- 560	2.91	154.11	H-Bond (Protein Donor)	false
O2A	OE1	GLN- 560	2.68	145.82	H-Bond (Ligand Donor)	false
O3A	NH1	ARG- 561	3.24	135.22	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 561	3.2	146.1	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 561	3.1	151.92	H-Bond (Protein Donor)	false
N1	OE2	GLU- 620	2.68	156.99	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 620	3.03	134.07	H-Bond (Ligand Donor)	false
O6	N	GLN- 639	2.71	177.14	H-Bond (Protein Donor)	false
C2'	CG	PRO- 644	4.18	0	Hydrophobic	false