scPDB - 3g07 entry

Protein Data Bank Entry:

PDB ID : 3g07

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2009-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	7SK snRNA methylphosphate capping enzyme
ID:	MEPCE_HUMAN
AC:	Q7L2J0
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	81.636
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.490	303.750

% Hydrophobic	% Polar
53.33	46.67
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	52.23 %
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
11.4212	76.182	19.3441

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
N	O	GLY- 451	2.83	139.96	H-Bond (Ligand Donor)	false
CB	CB	ASN- 453	3.94	0	Hydrophobic	false
O3'	ND2	ASN- 453	2.94	132.52	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 474	2.84	170.68	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 474	3.46	123.11	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 474	3.5	151.85	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 474	2.62	147.37	H-Bond (Ligand Donor)	false
N3	N	ILE- 475	3.15	128.95	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 479	4.4	0	Hydrophobic	false
N6	OD1	ASN- 559	2.65	130.73	H-Bond (Ligand Donor)	false
N1	N	TYR- 560	3.1	173.52	H-Bond (Protein Donor)	false
CG	CB	SER- 582	3.97	0	Hydrophobic	false
CE	CB	SER- 582	4.22	0	Hydrophobic	false
CE	CE2	TRP- 586	4.26	0	Hydrophobic	false