scPDB - 1kvk entry

Protein Data Bank Entry:

PDB ID : 1kvk

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2002-01-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mevalonate kinase
ID:	KIME_RAT
AC:	P17256
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.7.1.36

Chains:

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

Ligand binding site composition:

B-Factor:	44.758
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.067	506.250

% Hydrophobic	% Polar
48.67	51.33
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	56.05 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
42.6557	28.8025	15.3066

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
O2G	NZ	LYS- 13	2.79	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 13	3.73	0	Ionic (Protein Cationic)	false
C2'	CB	GLU- 105	3.88	0	Hydrophobic	false
O2'	OG	SER- 108	2.55	157.37	H-Bond (Ligand Donor)	false
N6	OG	SER- 135	2.97	142.31	H-Bond (Ligand Donor)	false
O2B	N	GLY- 140	2.81	136.63	H-Bond (Protein Donor)	false
O2G	N	GLY- 144	3.49	146.06	H-Bond (Protein Donor)	false
O2B	OG	SER- 145	3.21	133.19	H-Bond (Protein Donor)	false
O1B	N	SER- 146	2.84	167.48	H-Bond (Protein Donor)	false
C1'	CB	SER- 146	3.83	0	Hydrophobic	false
C4'	CB	SER- 146	3.63	0	Hydrophobic	false
C1'	CD1	ILE- 196	4.06	0	Hydrophobic	false
C4'	CD1	ILE- 196	3.38	0	Hydrophobic	false
O3G	MG	MG- 536	2.78	0	Metal Acceptor	false
O2B	O	HOH- 1064	3	163.89	H-Bond (Protein Donor)	false