scPDB - 4gek entry

Protein Data Bank Entry:

PDB ID : 4gek

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carboxy-S-adenosyl-L-methionine synthase
ID:	C3T5M2_ECOLX
AC:	C3T5M2
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.835
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.840	759.375

% Hydrophobic	% Polar
45.33	54.67
According to VolSite

Ligand :

HET Code:	GEK
Formula:	C16H22N6O7S
Molecular weight:	442.447 g/mol
DrugBank ID:	-
Buried Surface Area:	78.53 %
Polar Surface area:	229.9 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
19.6488	-18.6193	-22.158

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
C2'	CE2	PHE- 20	3.58	0	Hydrophobic	false
C3'	CZ	PHE- 20	3.59	0	Hydrophobic	false
CB	CZ	PHE- 28	3.85	0	Hydrophobic	false
SD	CZ	PHE- 28	3.74	0	Hydrophobic	false
O	OH	TYR- 39	2.66	162.76	H-Bond (Protein Donor)	false
N	O	GLY- 64	2.84	163.95	H-Bond (Ligand Donor)	false
SD	CB	SER- 66	4.32	0	Hydrophobic	false
CB	CB	SER- 66	3.96	0	Hydrophobic	false
O3'	OG	SER- 66	2.77	162.78	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 89	2.67	160	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 89	3.43	125.78	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 89	2.7	177.13	H-Bond (Ligand Donor)	false
N3	N	ASN- 90	3.2	146.31	H-Bond (Protein Donor)	false
N6	OD2	ASP- 117	3.02	172.26	H-Bond (Ligand Donor)	false
N1	N	ILE- 118	3.11	171.34	H-Bond (Protein Donor)	false
N	O	ASN- 132	2.92	164.85	H-Bond (Ligand Donor)	false
OXT	ND2	ASN- 132	2.8	173.47	H-Bond (Protein Donor)	false
CE	CB	PHE- 133	3.77	0	Hydrophobic	false
C5'	CE1	PHE- 137	3.59	0	Hydrophobic	false
OZ1	NH1	ARG- 199	3.35	134.81	H-Bond (Protein Donor)	false
OZ1	NH2	ARG- 199	2.96	152.99	H-Bond (Protein Donor)	false
OZ2	NH2	ARG- 199	3.47	141.98	H-Bond (Protein Donor)	false
OZ1	CZ	ARG- 199	3.58	0	Ionic (Protein Cationic)	false
N	O	HOH- 401	3.04	124.96	H-Bond (Ligand Donor)	false
O	O	HOH- 405	2.85	161.36	H-Bond (Protein Donor)	false