scPDB - 3ake entry

Protein Data Bank Entry:

PDB ID : 3ake

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2010-07-12

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_THET8
AC:	Q5SL35
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.171
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.820	1353.375

% Hydrophobic	% Polar
36.66	63.34
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	66.67 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
36.4043	11.9242	5.06643

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
O3P	NZ	LYS- 15	2.75	173.34	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 15	2.75	0	Ionic (Protein Cationic)	false
N4	OG	SER- 33	2.97	135.17	H-Bond (Ligand Donor)	false
C4'	CB	TYR- 37	4.36	0	Hydrophobic	false
C1'	CG	TYR- 37	3.96	0	Hydrophobic	false
O1P	NE	ARG- 38	3	168.09	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 38	3.46	137.55	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 38	3.69	0	Ionic (Protein Cationic)	false
C5'	CG	ARG- 38	4.2	0	Hydrophobic	false
C4'	CG2	VAL- 97	3.61	0	Hydrophobic	false
C1'	CB	ALA- 101	3.92	0	Hydrophobic	false
N3	NH1	ARG- 107	3.07	156.96	H-Bond (Protein Donor)	false
O2	NH1	ARG- 107	3.45	133.23	H-Bond (Protein Donor)	false
O2	NH2	ARG- 107	2.84	170.84	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 126	3.18	157.65	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 126	3.07	123.9	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 126	3.11	0	Ionic (Protein Cationic)	false
N4	OD1	ASP- 127	2.97	164.22	H-Bond (Ligand Donor)	false
O3P	O	HOH- 230	2.63	167.7	H-Bond (Protein Donor)	false