scPDB - 4u0m entry

Protein Data Bank Entry:

PDB ID : 4u0m

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-07-12

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:	32.308
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	ATP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.639	594.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	62.53 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
70.9223	9.87269	148.442

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
C4'	CG	GLN- 112	4.38	0	Hydrophobic	false
O2G	OG	SER- 114	2.55	153.95	H-Bond (Protein Donor)	false
O2B	N	SER- 114	3.11	155.82	H-Bond (Protein Donor)	false
O1B	OH	TYR- 117	2.83	155.09	H-Bond (Protein Donor)	false
O3'	OH	TYR- 117	3.18	160.7	H-Bond (Ligand Donor)	false
C2'	CG1	VAL- 264	4.18	0	Hydrophobic	false
O1G	NZ	LYS- 287	3.87	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 287	2.85	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 287	2.85	158.39	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 287	3.49	138.54	H-Bond (Protein Donor)	false
O1G	OG	SER- 301	2.91	146.57	H-Bond (Protein Donor)	false
O3B	OG	SER- 301	3.03	140.23	H-Bond (Protein Donor)	false
N1	OD2	ASP- 348	2.87	155.25	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 348	3.19	137.07	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 348	3.08	140.45	H-Bond (Ligand Donor)	false
C5'	C3'	ATP- 502	3.47	0	Hydrophobic	false
C4'	C2'	ATP- 502	3.87	0	Hydrophobic	false
C1'	C2'	ATP- 502	4.37	0	Hydrophobic	false
O3G	MG	MG- 503	2.31	0	Metal Acceptor	false
O2B	MG	MG- 503	2.14	0	Metal Acceptor	false
O2A	MG	MG- 503	2.04	0	Metal Acceptor	false
O1A	O	HOH- 667	3.48	158.56	H-Bond (Protein Donor)	false