scPDB - 5c8w entry

Protein Data Bank Entry:

PDB ID : 5c8w

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cGMP-dependent protein kinase 2
ID:	KGP2_HUMAN
AC:	Q13237
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.12

Chains:

Chain Name:	Percentage of Residues within binding site
C	23 %
E	77 %

Ligand binding site composition:

B-Factor:	28.480
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.201	705.375

% Hydrophobic	% Polar
44.02	55.98
According to VolSite

Ligand :

HET Code:	PCG
Formula:	C10H11N5O7P
Molecular weight:	344.197 g/mol
DrugBank ID:	-
Buried Surface Area:	71.09 %
Polar Surface area:	183.16 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	4
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
21.3729	9.52674	-38.0661

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
C5'	CG2	ILE- 196	3.99	0	Hydrophobic	false
N7	OG	SER- 223	3.13	141.76	H-Bond (Protein Donor)	false
C1'	CB	PHE- 231	4.46	0	Hydrophobic	false
O2'	N	GLY- 232	3.13	170.09	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 233	2.7	134.01	H-Bond (Ligand Donor)	false
C3'	CD1	LEU- 234	3.96	0	Hydrophobic	false
O1A	N	ALA- 235	2.97	166.02	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 242	2.86	149.1	H-Bond (Protein Donor)	false
O2A	OG1	THR- 243	2.88	147.62	H-Bond (Protein Donor)	false
O2A	N	THR- 243	2.93	169.59	H-Bond (Protein Donor)	false
N2	OG1	THR- 243	2.9	176.43	H-Bond (Ligand Donor)	false
C5'	CG2	VAL- 246	3.95	0	Hydrophobic	false