scPDB - 4n49 entry

Protein Data Bank Entry:

PDB ID : 4n49

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-10-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
ID:	CMTR1_HUMAN
AC:	Q8N1G2
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.57

Chains:

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

Ligand binding site composition:

B-Factor:	10.105
Number of residues:	33
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.426	529.875

% Hydrophobic	% Polar
41.40	58.60
According to VolSite

Ligand :

HET Code:	MGT
Formula:	C11H16N5O14P3
Molecular weight:	535.191 g/mol
DrugBank ID:	DB03358
Buried Surface Area:	46.98 %
Polar Surface area:	324.22 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.2194	26.2545	32.2434

Binding mode :

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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
CM7	CB	PHE- 206	4.47	0	Hydrophobic	false
N1	OD1	ASP- 207	2.72	169.77	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 207	3.43	126.43	H-Bond (Ligand Donor)	false
CM7	SD	MET- 214	4.23	0	Hydrophobic	false
O2G	NH2	ARG- 218	3.45	164.25	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 218	2.91	150.77	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 218	3.83	0	Ionic (Protein Cationic)	false
C2'	CG	GLU- 373	4.47	0	Hydrophobic	false
N2	OD1	ASN- 374	2.78	162.27	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 438	4.3	0	Hydrophobic	false
O2B	ND2	ASN- 439	2.93	167.1	H-Bond (Protein Donor)	false
C3'	CB	ASN- 439	3.79	0	Hydrophobic	false
C4'	CD2	LEU- 511	4.01	0	Hydrophobic	false
O2'	O	HOH- 865	2.81	179.97	H-Bond (Protein Donor)	false
O3'	O	HOH- 928	2.78	177.77	H-Bond (Ligand Donor)	false