scPDB - 1nhk entry

Protein Data Bank Entry:

PDB ID : 1nhk

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1994-12-09

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_MYXXA
AC:	P15266
Organism:	Myxococcus xanthus
Reign:	Bacteria
TaxID:	34
EC Number:	2.7.4.6

Chains:

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

Ligand binding site composition:

B-Factor:	22.464
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.479	651.375

% Hydrophobic	% Polar
48.70	51.30
According to VolSite

Ligand :

HET Code:	CMP
Formula:	C10H11N5O6P
Molecular weight:	328.198 g/mol
DrugBank ID:	DB02527
Buried Surface Area:	53.34 %
Polar Surface area:	167.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
30.8105	56.1161	16.843

Binding mode :

What is Poseview ?

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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
O1P	NZ	LYS- 11	2.92	143.04	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 11	3.44	147.3	H-Bond (Protein Donor)	false
O1P	OH	TYR- 51	2.91	130.94	H-Bond (Protein Donor)	false
C5'	CE1	TYR- 51	3.96	0	Hydrophobic	false
C1'	CD1	PHE- 59	4.25	0	Hydrophobic	false
C5'	CE1	PHE- 59	4.36	0	Hydrophobic	false
C5'	CD2	LEU- 63	3.68	0	Hydrophobic	false
C4'	CD1	LEU- 63	3.78	0	Hydrophobic	false
C2'	CG2	THR- 93	3.81	0	Hydrophobic	false
C2'	CG1	ILE- 111	4.38	0	Hydrophobic	false
O2'	O	ILE- 111	2.78	160.69	H-Bond (Ligand Donor)	false
O2'	O	HOH- 194	2.98	155.8	H-Bond (Protein Donor)	false