scPDB - 2cmk entry

Protein Data Bank Entry:

PDB ID : 2cmk

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1998-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytidylate kinase
ID:	KCY_ECOLI
AC:	P0A6I0
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.7.4.25

Chains:

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

Ligand binding site composition:

B-Factor:	29.958
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.447	1066.500

% Hydrophobic	% Polar
29.75	70.25
According to VolSite

Ligand :

HET Code:	CDP
Formula:	C9H12N3O11P2
Molecular weight:	400.153 g/mol
DrugBank ID:	DB04555
Buried Surface Area:	65.17 %
Polar Surface area:	249.77 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
59.6169	55.9581	21.9874

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
O3B	OG	SER- 14	2.62	141.75	H-Bond (Protein Donor)	false
O2B	OG	SER- 14	3.48	139.34	H-Bond (Protein Donor)	false
N4	OG	SER- 36	2.64	140.89	H-Bond (Ligand Donor)	false
O3A	NE	ARG- 41	3.41	124.56	H-Bond (Protein Donor)	false
O2A	NE	ARG- 41	3.16	158.94	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 41	3.98	0	Ionic (Protein Cationic)	false
C4'	CB	ALA- 100	4.07	0	Hydrophobic	false
C1'	CB	ALA- 104	4.07	0	Hydrophobic	false
O2	NH1	ARG- 110	2.84	177.72	H-Bond (Protein Donor)	false
N3	NH2	ARG- 110	3.21	165.34	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 131	3.8	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 131	3.13	0	Ionic (Protein Cationic)	false
O3B	NH2	ARG- 131	2.62	125.57	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 131	2.8	131.36	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 131	2.67	136.8	H-Bond (Protein Donor)	false
C2'	CG	ARG- 131	4.09	0	Hydrophobic	false
N4	OD1	ASP- 132	3	170.19	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 185	2.66	136.25	H-Bond (Ligand Donor)	false
O2'	NH1	ARG- 188	3.22	146.2	H-Bond (Protein Donor)	false
O2	NH2	ARG- 188	3.18	123.2	H-Bond (Protein Donor)	false
O2	NH1	ARG- 188	3.06	125.64	H-Bond (Protein Donor)	false