scPDB - 2v2q entry

Protein Data Bank Entry:

PDB ID : 2v2q

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
ID:	ISPE_AQUAE
AC:	O67060
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.950
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.902	762.750

% Hydrophobic	% Polar
43.36	56.64
According to VolSite

Ligand :

HET Code:	NVG
Formula:	C19H22N6O5
Molecular weight:	414.415 g/mol
DrugBank ID:	-
Buried Surface Area:	49.44 %
Polar Surface area:	166.16 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-31.6571	0.3718	7.3994

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
CBC	CE2	TYR- 24	4.49	0	Hydrophobic	false
CAH	CE2	TYR- 24	3.38	0	Hydrophobic	false
CBA	CZ	TYR- 24	3.82	0	Hydrophobic	false
OAC	ND1	HIS- 25	2.99	172.89	H-Bond (Protein Donor)	false
NAO	N	HIS- 25	3.02	150.78	H-Bond (Protein Donor)	false
NAA	O	HIS- 25	2.82	164.03	H-Bond (Ligand Donor)	false
CAK	CB	SER- 128	4.31	0	Hydrophobic	false
CAH	CB	ALA- 129	3.62	0	Hydrophobic	false
NAA	O	LYS- 145	3.26	161.58	H-Bond (Ligand Donor)	false
CBC	CG2	THR- 171	4.42	0	Hydrophobic	false
CAL	CB	THR- 171	3.67	0	Hydrophobic	false
CBC	CD1	TYR- 175	3.54	0	Hydrophobic	false