scPDB - 4ymg entry

Protein Data Bank Entry:

PDB ID : 4ymg

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-03-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative SAM-dependent O-methyltranferase
ID:	Q9HGR1_PODAS
AC:	Q9HGR1
Organism:	Podospora anserina
Reign:	Eukaryota
TaxID:	5145
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.936
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.960	1589.625

% Hydrophobic	% Polar
39.28	60.72
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	71.63 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-3.57415	2.91526	-21.3277

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
C3'	CD	LYS- 47	4.39	0	Hydrophobic	false
SD	CB	LYS- 47	3.91	0	Hydrophobic	false
O	N	SER- 49	3.19	163.16	H-Bond (Protein Donor)	false
N	O	GLY- 73	2.78	151.96	H-Bond (Ligand Donor)	false
SD	CB	TYR- 75	3.94	0	Hydrophobic	false
C4'	CB	TYR- 75	4.46	0	Hydrophobic	false
C3'	CD1	TYR- 75	4.23	0	Hydrophobic	false
CB	CB	TYR- 75	3.57	0	Hydrophobic	false
N	OG	SER- 79	2.74	165.17	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 98	2.66	160.29	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 98	3.22	129.08	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 98	2.52	156.15	H-Bond (Ligand Donor)	false
N3	N	TYR- 99	3.38	121.21	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 99	3.72	0	Aromatic Face/Face	false
C2'	CE2	TYR- 99	3.91	0	Hydrophobic	false
N1	N	ALA- 127	2.85	164.34	H-Bond (Protein Donor)	false
N6	OE1	GLU- 128	3.02	157.38	H-Bond (Ligand Donor)	false
N	OD2	ASP- 144	2.66	148.43	H-Bond (Ligand Donor)	false
N	OD2	ASP- 144	2.66	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 144	4.47	0	Hydrophobic	false
C1'	CB	ALA- 145	4.31	0	Hydrophobic	false
O	O	HOH- 1161	2.72	161.58	H-Bond (Protein Donor)	false