scPDB - 3q8u entry

Protein Data Bank Entry:

PDB ID : 3q8u

Resolution :2.220 Å

Experimental Method : X-ray

Deposition Date : 2011-01-07

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_STAAC
AC:	Q5HFV4
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93062
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.544
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.278	509.625

% Hydrophobic	% Polar
46.36	53.64
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	43.79 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
9.64778	52.3526	-44.2654

Binding mode :

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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
O2'	NZ	LYS- 9	3.18	122.07	H-Bond (Protein Donor)	false
C5'	CE1	PHE- 57	4.39	0	Hydrophobic	false
C1'	CE1	PHE- 57	4.1	0	Hydrophobic	false
DuAr	DuAr	PHE- 57	3.81	0	Aromatic Face/Face	false
C1'	CG	LEU- 61	4.35	0	Hydrophobic	false
O1B	OG1	THR- 91	2.71	153	H-Bond (Protein Donor)	false
C3'	CG2	THR- 91	3.46	0	Hydrophobic	false
O1B	NH1	ARG- 102	2.64	134.08	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 102	3.52	0	Ionic (Protein Cationic)	false
O2'	O	VAL- 109	3.28	133.77	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 112	3.04	172.07	H-Bond (Protein Donor)	false
O3B	O	HOH- 160	2.63	179.98	H-Bond (Protein Donor)	false
O2B	O	HOH- 162	2.77	179.95	H-Bond (Protein Donor)	false