scPDB - 2v2z entry

Protein Data Bank Entry:

PDB ID : 2v2z

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2007-06-08

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:	31.137
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.807	533.250

% Hydrophobic	% Polar
44.30	55.70
According to VolSite

Ligand :

HET Code:	CDM
Formula:	C14H23N3O14P2
Molecular weight:	519.292 g/mol
DrugBank ID:	DB03687
Buried Surface Area:	62.06 %
Polar Surface area:	296.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
167.14	67.6621	60.5825

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
O3M	NZ	LYS- 9	3.36	161.14	H-Bond (Protein Donor)	false
O4M	NZ	LYS- 9	3.41	135.65	H-Bond (Protein Donor)	false
O4M	ND2	ASN- 11	2.94	150.49	H-Bond (Protein Donor)	false
C4M	CD1	LEU- 14	3.41	0	Hydrophobic	false
C2'	CE2	TYR- 24	3.96	0	Hydrophobic	false
C3'	CZ	TYR- 24	3.93	0	Hydrophobic	false
N3	N	HIS- 25	2.95	150.2	H-Bond (Protein Donor)	false
O2	ND1	HIS- 25	2.75	171.68	H-Bond (Protein Donor)	false
N4	O	HIS- 25	3.04	163.99	H-Bond (Ligand Donor)	false
C4M	CD1	ILE- 27	4.47	0	Hydrophobic	false
O1B	N	ALA- 129	2.84	164.01	H-Bond (Protein Donor)	false
O3M	OD2	ASP- 130	2.78	173.5	H-Bond (Ligand Donor)	false
O4M	OD1	ASP- 130	2.92	153.99	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 171	3.91	0	Hydrophobic	false
C1M	CG2	THR- 171	4.01	0	Hydrophobic	false
C5M	CG2	THR- 171	4.21	0	Hydrophobic	false
C1'	CB	TYR- 175	3.81	0	Hydrophobic	false
C5M	CE1	TYR- 175	3.85	0	Hydrophobic	false
O2M	OH	TYR- 175	2.7	141.18	H-Bond (Protein Donor)	false
C5M	CD1	LEU- 208	3.74	0	Hydrophobic	false
C5M	CB	SER- 238	4.36	0	Hydrophobic	false