scPDB - 4xvy entry

Protein Data Bank Entry:

PDB ID : 4xvy

Resolution :2.420 Å

Experimental Method : X-ray

Deposition Date : 2015-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mycinamicin III 3''-O-methyltransferase
ID:	MYCF_MICGR
AC:	Q49492
Organism:	Micromonospora griseorubida
Reign:	Bacteria
TaxID:	28040
EC Number:	2.1.1.237

Chains:

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

Ligand binding site composition:

B-Factor:	52.692
Number of residues:	47
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.709	556.875

% Hydrophobic	% Polar
50.91	49.09
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	81.51 %
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
-12.3971	-9.83723	-27.1023

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
O	OG1	THR- 55	2.99	140.56	H-Bond (Protein Donor)	false
OXT	OG1	THR- 55	2.55	150.62	H-Bond (Protein Donor)	false
CB	CG	MET- 56	3.82	0	Hydrophobic	false
SD	SD	MET- 56	4.45	0	Hydrophobic	false
O	N	MET- 56	2.69	169.44	H-Bond (Protein Donor)	false
N	OE2	GLU- 83	3.68	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 83	2.8	0	Ionic (Ligand Cationic)	false
N	O	GLY- 85	2.86	165.92	H-Bond (Ligand Donor)	false
SD	CB	TRP- 87	4.21	0	Hydrophobic	false
CB	CB	TRP- 87	3.58	0	Hydrophobic	false
O3'	N	TRP- 87	3.49	129.26	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 113	2.93	171.66	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 113	3.42	132.93	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 113	2.62	163.42	H-Bond (Ligand Donor)	false
N3	N	SER- 114	2.98	153.68	H-Bond (Protein Donor)	false
C5'	CZ	PHE- 118	4.25	0	Hydrophobic	false
SD	CD1	LEU- 143	3.94	0	Hydrophobic	false
C3'	CD2	LEU- 143	3.75	0	Hydrophobic	false
N1	N	PHE- 171	3.08	139.42	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 171	3.4	0	Aromatic Face/Face	false
N	OD2	ASP- 189	2.71	170.75	H-Bond (Ligand Donor)	false
N	OD2	ASP- 189	2.71	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 189	4.2	0	Hydrophobic	false
N6	O	HOH- 408	2.93	173.15	H-Bond (Ligand Donor)	false