scPDB - 3fbc entry

Protein Data Bank Entry:

PDB ID : 3fbc

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-11-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nucleoside diphosphate kinase
ID:	NDK_MIMIV
AC:	Q5UQL3
Organism:	Acanthamoeba polyphaga mimivirus
Reign:	Viruses
TaxID:	212035
EC Number:	2.7.4.6

Chains:

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

Ligand binding site composition:

B-Factor:	54.523
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.095	378.000

% Hydrophobic	% Polar
53.57	46.43
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	47.89 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-13.8929	14.7571	16.4983

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
C4'	CE2	TYR- 50	4.28	0	Hydrophobic	false
C1'	CD1	TYR- 58	4.47	0	Hydrophobic	false
C5M	CE2	TYR- 58	3.6	0	Hydrophobic	false
C4'	CD1	LEU- 62	4.09	0	Hydrophobic	false
C1'	CG	LEU- 62	3.78	0	Hydrophobic	false
O1B	NH2	ARG- 99	3.15	134.95	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 99	3.07	164.59	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 99	3.87	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 99	3.93	0	Ionic (Protein Cationic)	false
O3'	ND2	ASN- 109	3.16	153.32	H-Bond (Protein Donor)	false
O2B	MG	MG- 160	2.69	0	Metal Acceptor	false