scPDB - 3swr entry

Protein Data Bank Entry:

PDB ID : 3swr

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2011-07-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA (cytosine-5)-methyltransferase 1
ID:	DNMT1_HUMAN
AC:	P26358
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.37

Chains:

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

Ligand binding site composition:

B-Factor:	45.339
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.919	948.375

% Hydrophobic	% Polar
42.70	57.30
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	66.5 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
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
-4.89852	-1.35974	33.0021

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
N	O	HOH- 213	3.23	166.86	H-Bond (Ligand Donor)	false
OXT	O	HOH- 258	2.76	141.2	H-Bond (Protein Donor)	false
C1'	CB	PHE- 1145	4.47	0	Hydrophobic	false
C4'	CB	PHE- 1145	4	0	Hydrophobic	false
OXT	N	GLY- 1149	3.47	146.04	H-Bond (Protein Donor)	false
OXT	N	GLY- 1150	3.36	129.94	H-Bond (Protein Donor)	false
O	N	LEU- 1151	2.87	152.96	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 1168	2.96	125.81	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 1168	2.74	169.29	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 1168	2.69	163.67	H-Bond (Ligand Donor)	false
N3	N	MET- 1169	3.21	174.01	H-Bond (Protein Donor)	false
N1	N	CYS- 1191	3.33	157.9	H-Bond (Protein Donor)	false
C5'	CG	PRO- 1225	4.31	0	Hydrophobic	false
N	OE1	GLU- 1266	2.92	143.3	H-Bond (Ligand Donor)	false
N	OE1	GLU- 1266	2.92	0	Ionic (Ligand Cationic)	false
NE	O	ASN- 1578	3.42	130.36	H-Bond (Ligand Donor)	false
O	N	VAL- 1580	2.85	166.28	H-Bond (Protein Donor)	false