scPDB - 3fbe entry

Protein Data Bank Entry:

PDB ID : 3fbe

Resolution :2.400 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
B	100 %

Ligand binding site composition:

B-Factor:	41.989
Number of residues:	22
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.091	354.375

% Hydrophobic	% Polar
51.43	48.57
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	38.28 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
70.4454	64.5781	67.2597

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
O3'	NE2	HIS- 53	3.24	144.77	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 86	3.51	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 86	2.51	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 86	2.96	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 86	2.7	123.01	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 86	2.53	128.04	H-Bond (Protein Donor)	false
O1B	NE2	GLN- 89	2.69	141.31	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 99	2.99	126.03	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 99	3.19	143.49	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 99	3.01	153.73	H-Bond (Protein Donor)	false