scPDB - 4lj3 entry

Protein Data Bank Entry:

PDB ID : 4lj3

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2013-07-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclic di-GMP phosphodiesterase YahA
ID:	YAHA_ECOLI
AC:	P21514
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	12.370
Number of residues:	49
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	3
Water Molecules:	6
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.357	482.625

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	63.79 %
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
16.6833	6.7592	24.4876

Binding mode :

What is Poseview ?

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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
N7	NE2	GLN- 127	3.26	162.2	H-Bond (Protein Donor)	false
C5'	CD2	LEU- 143	4.43	0	Hydrophobic	false
C3A	CD2	LEU- 143	4.37	0	Hydrophobic	false
C2'	CD1	LEU- 143	3.67	0	Hydrophobic	false
N71	N	VAL- 144	3.25	168.81	H-Bond (Protein Donor)	false
O11	NH1	ARG- 145	2.86	144.32	H-Bond (Protein Donor)	false
O11	NH2	ARG- 145	3.04	136.03	H-Bond (Protein Donor)	false
C5A	CG	PRO- 156	4.03	0	Hydrophobic	false
C1A	CB	PRO- 156	4.3	0	Hydrophobic	false
N3	NZ	LYS- 286	3.01	168.66	H-Bond (Protein Donor)	false
N1	OE2	GLU- 322	2.62	155.58	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 322	2.92	136.82	H-Bond (Ligand Donor)	false
O6	N	TYR- 341	2.8	176.69	H-Bond (Protein Donor)	false
C2'	CG	PRO- 346	4.3	0	Hydrophobic	false
O2P	CA	CA- 402	2.26	0	Metal Acceptor	false
O1P	CA	CA- 403	2.29	0	Metal Acceptor	false
N21	O	HOH- 507	2.83	154.18	H-Bond (Ligand Donor)	false
O21	O	HOH- 512	2.67	146.02	H-Bond (Protein Donor)	false
N2	O	HOH- 685	2.89	127.1	H-Bond (Ligand Donor)	false