scPDB - 2dr8 entry

Protein Data Bank Entry:

PDB ID : 2dr8

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-06-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CCA-adding enzyme
ID:	CCA_ARCFU
AC:	O28126
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	2.7.7.72

Chains:

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

Ligand binding site composition:

B-Factor:	41.139
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.023	675.000

% Hydrophobic	% Polar
36.50	63.50
According to VolSite

Ligand :

HET Code:	CTP
Formula:	C9H12N3O14P3
Molecular weight:	479.125 g/mol
DrugBank ID:	DB02431
Buried Surface Area:	47.52 %
Polar Surface area:	308.95 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.2088	-4.08883	-32.3978

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
O2B	N	SER- 47	3.07	170.99	H-Bond (Protein Donor)	false
O2B	OG	SER- 47	3.34	158.47	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 50	2.99	158.21	H-Bond (Protein Donor)	false
C4'	CG2	THR- 130	4.3	0	Hydrophobic	false
C1'	CG2	THR- 130	4.02	0	Hydrophobic	false
C2'	CB	HIS- 133	4.43	0	Hydrophobic	false
O2'	ND1	HIS- 133	2.71	153.65	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 152	3.19	169.19	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 152	3.19	0	Ionic (Protein Cationic)	false
O1G	OH	TYR- 161	3.47	155.88	H-Bond (Protein Donor)	false
O2G	OH	TYR- 161	3.06	133.07	H-Bond (Protein Donor)	false
C3'	CB	TYR- 173	3.57	0	Hydrophobic	false
N3	NH2	ARG- 224	2.69	143.01	H-Bond (Protein Donor)	false
O2	NH1	ARG- 224	3.1	139.85	H-Bond (Protein Donor)	false
O2	NH2	ARG- 224	2.98	145.2	H-Bond (Protein Donor)	false
O2B	MG	MG- 503	2.78	0	Metal Acceptor	false
O3G	MG	MG- 503	2.7	0	Metal Acceptor	false