scPDB - 4iwn entry

Protein Data Bank Entry:

PDB ID : 4iwn

Resolution :1.730 Å

Experimental Method : X-ray

Deposition Date : 2013-01-24

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:	CMOA_ECOLI
AC:	P76290
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.814
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.859	762.750

% Hydrophobic	% Polar
55.75	44.25
According to VolSite

Ligand :

HET Code:	GEK
Formula:	C16H22N6O7S
Molecular weight:	442.447 g/mol
DrugBank ID:	-
Buried Surface Area:	72.83 %
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
21.7495	-0.553267	39.9511

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
CB	CZ	PHE- 28	3.92	0	Hydrophobic	false
SD	CZ	PHE- 28	3.9	0	Hydrophobic	false
CE	CD1	ILE- 32	4.44	0	Hydrophobic	false
O	OH	TYR- 39	2.56	166.57	H-Bond (Protein Donor)	false
N	O	GLY- 64	2.92	159.49	H-Bond (Ligand Donor)	false
SD	CB	SER- 66	4.26	0	Hydrophobic	false
CB	CB	SER- 66	3.94	0	Hydrophobic	false
O3'	OG	SER- 66	2.67	165.71	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 89	2.65	153.69	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 89	2.59	165.98	H-Bond (Ligand Donor)	false
N3	N	ASN- 90	3.18	138.66	H-Bond (Protein Donor)	false
N6	OD1	ASP- 117	3.12	164.69	H-Bond (Ligand Donor)	false
N1	N	ILE- 118	3	168.02	H-Bond (Protein Donor)	false
N	O	ASN- 132	2.81	171.81	H-Bond (Ligand Donor)	false
OXT	ND2	ASN- 132	2.78	175.74	H-Bond (Protein Donor)	false
CE	CB	PHE- 133	3.86	0	Hydrophobic	false
CE	CE1	PHE- 137	3.92	0	Hydrophobic	false
C5'	CE1	PHE- 137	3.59	0	Hydrophobic	false
OZ1	NH2	ARG- 199	2.96	172.61	H-Bond (Protein Donor)	false
OZ2	NH1	ARG- 199	2.84	172.23	H-Bond (Protein Donor)	false
OZ1	CZ	ARG- 199	3.74	0	Ionic (Protein Cationic)	false
OZ2	CZ	ARG- 199	3.74	0	Ionic (Protein Cationic)	false
O	O	HOH- 405	2.87	179.95	H-Bond (Protein Donor)	false
N	O	HOH- 408	3.09	120.87	H-Bond (Ligand Donor)	false