scPDB - 2dxf entry

Protein Data Bank Entry:

PDB ID : 2dxf

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-08-25

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_PYRHO
AC:	O58429
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	2.7.4.6

Chains:

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

Ligand binding site composition:

B-Factor:	17.180
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.198	334.125

% Hydrophobic	% Polar
51.52	48.48
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	47.48 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.3396	27.3215	9.24971

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
C5'	CE1	TYR- 55	4.29	0	Hydrophobic	false
C1'	CE1	PHE- 63	3.94	0	Hydrophobic	false
DuAr	DuAr	PHE- 63	3.58	0	Aromatic Face/Face	false
C4'	CD1	LEU- 67	4.13	0	Hydrophobic	false
C1'	CD1	LEU- 67	3.94	0	Hydrophobic	false
C3'	CG2	THR- 97	3.78	0	Hydrophobic	false
C2'	CB	ILE- 119	3.98	0	Hydrophobic	false
O2'	O	ILE- 119	3.31	149.18	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 121	2.51	143.18	H-Bond (Protein Donor)	false