scPDB - 5c6c entry

Protein Data Bank Entry:

PDB ID : 5c6c

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2015-06-22

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
A	77 %
B	23 %

Ligand binding site composition:

B-Factor:	30.619
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
1.002	529.875

% Hydrophobic	% Polar
51.59	48.41
According to VolSite

Ligand :

HET Code:	CMP
Formula:	C10H11N5O6P
Molecular weight:	328.198 g/mol
DrugBank ID:	DB02527
Buried Surface Area:	74.62 %
Polar Surface area:	167.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
9.31077	26.0508	58.6255

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
C5'	CG2	ILE- 196	3.88	0	Hydrophobic	false
C4'	CD1	ILE- 196	4.32	0	Hydrophobic	false
C1'	CG1	VAL- 215	4.42	0	Hydrophobic	false
O2'	N	GLY- 232	3.05	157.02	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 233	2.72	160.41	H-Bond (Ligand Donor)	false
C3'	CD1	LEU- 234	3.93	0	Hydrophobic	false
O1P	N	ALA- 235	3.01	160.13	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 242	2.86	155.42	H-Bond (Protein Donor)	false
O2P	OG1	THR- 243	2.8	163.79	H-Bond (Protein Donor)	false
O2P	N	THR- 243	2.9	163.98	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 246	4.31	0	Hydrophobic	false