scPDB - 4l7v entry

Protein Data Bank Entry:

PDB ID : 4l7v

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2013-06-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein-L-isoaspartate O-methyltransferase
ID:	PIMT_VIBC3
AC:	A5F9C1
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	345073
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.019
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.620	445.500

% Hydrophobic	% Polar
38.64	61.36
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.56 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-6.08485	14.3315	15.1458

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
N	OE1	GLU- 81	3.98	0	Ionic (Ligand Cationic)	false
O	OG	SER- 86	2.62	167	H-Bond (Protein Donor)	false
O	N	SER- 86	3.02	160.27	H-Bond (Protein Donor)	false
OXT	OG	SER- 86	3.4	125.33	H-Bond (Protein Donor)	false
OXT	N	GLN- 89	3.18	173.62	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 104	2.73	167.62	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 104	2.51	157.67	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 104	3.37	135.72	H-Bond (Ligand Donor)	false
C3'	CD1	LEU- 109	4.49	0	Hydrophobic	false
N6	OD1	ASP- 131	3.08	161.04	H-Bond (Ligand Donor)	false
N1	N	GLY- 132	2.68	156.56	H-Bond (Protein Donor)	false
N	OG1	THR- 148	3.4	162.75	H-Bond (Ligand Donor)	false
CG	CB	THR- 148	3.86	0	Hydrophobic	false
C5'	CG2	VAL- 200	3.74	0	Hydrophobic	false
N7	N	VAL- 203	3.01	163.95	H-Bond (Protein Donor)	false
N6	O	VAL- 203	2.72	125.16	H-Bond (Ligand Donor)	false