scPDB - 4ckc entry

Protein Data Bank Entry:

PDB ID : 4ckc

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2014-01-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	mRNA-capping enzyme catalytic subunit
ID:	MCEL_VACCW
AC:	P04298
Organism:	Vaccinia virus )
Reign:	Viruses
TaxID:	10254
EC Number:	2.1.1.56

Chains:

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

Ligand binding site composition:

B-Factor:	23.367
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.876	1201.500

% Hydrophobic	% Polar
44.38	55.62
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	73.86 %
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
-4.59823	-31.1018	0.645231

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
N6	O	LEU- 549	3.09	136.15	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 550	3.29	157.25	H-Bond (Protein Donor)	false
SD	CE2	TYR- 555	3.68	0	Hydrophobic	false
C5'	CZ	TYR- 555	3.94	0	Hydrophobic	false
C2'	CG	TYR- 555	3.83	0	Hydrophobic	false
CB	CZ	PHE- 556	4.26	0	Hydrophobic	false
SD	CZ	PHE- 556	3.61	0	Hydrophobic	false
C3'	CE2	PHE- 556	3.98	0	Hydrophobic	false
O	NZ	LYS- 573	2.84	150.18	H-Bond (Protein Donor)	false
O	NZ	LYS- 573	2.84	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 573	3.35	0	Ionic (Protein Cationic)	false
N	O	ASP- 598	3.08	145.69	H-Bond (Ligand Donor)	false
C4'	CB	ASP- 598	4.31	0	Hydrophobic	false
C1'	CB	ASP- 598	4.12	0	Hydrophobic	false
O3'	OD2	ASP- 620	2.65	161.23	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 620	3.01	154.5	H-Bond (Ligand Donor)	false
N7	NH2	ARG- 655	2.83	149.81	H-Bond (Protein Donor)	false
N	O	GLN- 678	3.06	162.82	H-Bond (Ligand Donor)	false
CG	CB	PHE- 679	4.15	0	Hydrophobic	false
C5'	CB	ALA- 680	4.36	0	Hydrophobic	false
C5'	CE2	TYR- 683	4.23	0	Hydrophobic	false
DuAr	DuAr	TYR- 683	3.78	0	Aromatic Face/Face	false