scPDB - 4xj4 entry

Protein Data Bank Entry:

PDB ID : 4xj4

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2015-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclic GMP-AMP synthase
ID:	DNCV_VIBCH
AC:	Q9KVG7
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.690
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.590	648.000

% Hydrophobic	% Polar
35.42	64.58
According to VolSite

Ligand :

HET Code:	3AT
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB01860
Buried Surface Area:	47.1 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
18.3748	-29.2462	-18.4408

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
C4'	CG	GLN- 112	4.17	0	Hydrophobic	false
O2G	OG	SER- 114	2.63	170.36	H-Bond (Protein Donor)	false
O1B	N	SER- 114	2.84	157.44	H-Bond (Protein Donor)	false
O2B	OH	TYR- 117	2.83	144.1	H-Bond (Protein Donor)	false
C5'	CB	ASP- 133	4.46	0	Hydrophobic	false
C2'	CG1	VAL- 264	4.29	0	Hydrophobic	false
O2G	NZ	LYS- 287	2.82	153.16	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 287	2.82	0	Ionic (Protein Cationic)	false
O3G	OG	SER- 301	2.7	155.85	H-Bond (Protein Donor)	false
O3B	OG	SER- 301	3.39	120.66	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 302	4.2	0	Hydrophobic	false
O1G	MG	MG- 1008	2.16	0	Metal Acceptor	false
O1B	MG	MG- 1008	2.13	0	Metal Acceptor	false
O1A	MG	MG- 1008	2.34	0	Metal Acceptor	false