scPDB - 1yf3 entry

Protein Data Bank Entry:

PDB ID : 1yf3

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2004-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA adenine methylase
ID:	DMA_BPT4
AC:	P04392
Organism:	Enterobacteria phage T4
Reign:	Viruses
TaxID:	10665
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.475
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	577.125

% Hydrophobic	% Polar
46.20	53.80
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	84.5 %
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
10.7528	8.53623	32.5724

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
CB	CD2	TYR- 7	4.33	0	Hydrophobic	false
SD	CE2	TYR- 7	3.86	0	Hydrophobic	false
C3'	CE2	TYR- 7	4.2	0	Hydrophobic	false
O3'	OH	TYR- 7	2.68	138.36	H-Bond (Protein Donor)	false
O	N	LYS- 11	3.09	146.17	H-Bond (Protein Donor)	false
C4'	CB	PHE- 32	4.03	0	Hydrophobic	false
C1'	CD2	PHE- 32	3.94	0	Hydrophobic	false
OXT	N	GLY- 35	3.06	163.03	H-Bond (Protein Donor)	false
O	OG	SER- 37	2.87	165.98	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 50	2.59	159.86	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 50	2.58	146.95	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 50	3.44	153.67	H-Bond (Ligand Donor)	false
N3	N	ILE- 51	3.36	146.32	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 51	4.35	0	Hydrophobic	false
O2'	NE2	GLN- 52	3.06	164.75	H-Bond (Protein Donor)	false
N1	N	PHE- 157	2.88	136.65	H-Bond (Protein Donor)	false
N	OD1	ASP- 171	3.01	168.95	H-Bond (Ligand Donor)	false
N	OD1	ASP- 171	3.01	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 171	4.2	0	Hydrophobic	false
C5'	CG	PRO- 173	4.25	0	Hydrophobic	false
SD	CE1	TYR- 181	3.71	0	Hydrophobic	false
C5'	CE2	TYR- 181	4.12	0	Hydrophobic	false
C3'	CD1	TYR- 181	4.05	0	Hydrophobic	false
C2'	CB	TYR- 181	4.11	0	Hydrophobic	false
N	O	HOH- 499	2.72	155.22	H-Bond (Ligand Donor)	false