scPDB - 2pkm entry

Protein Data Bank Entry:

PDB ID : 2pkm

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosine kinase
ID:	ADOK_MYCTU
AC:	P9WID5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.7.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	28.200
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.438	813.375

% Hydrophobic	% Polar
31.95	68.05
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	80.56 %
Polar Surface area:	139.54 Å2

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

Mass center Coordinates

X	Y	Z
23.0212	4.95463	25.3303

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
N3	OG	SER- 8	2.63	150.19	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 12	2.7	165.46	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 12	3.37	131.18	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 12	2.76	173.49	H-Bond (Ligand Donor)	false
O3'	N	GLY- 48	2.99	145.84	H-Bond (Protein Donor)	false
O2'	N	GLY- 48	2.82	130.88	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 49	3.76	0	Hydrophobic	false
C4'	CG1	VAL- 49	4.33	0	Hydrophobic	false
O3'	ND2	ASN- 52	3.02	142.34	H-Bond (Protein Donor)	false
C4'	CE2	PHE- 102	4.48	0	Hydrophobic	false
C2'	CD2	PHE- 102	3.63	0	Hydrophobic	false
DuAr	DuAr	PHE- 116	3.62	0	Aromatic Face/Face	false
C2'	CE1	PHE- 116	4	0	Hydrophobic	false
O5'	NE2	GLN- 172	2.62	134.37	H-Bond (Protein Donor)	false
N6	OE1	GLN- 173	2.97	151.65	H-Bond (Ligand Donor)	false
N1	NE2	GLN- 173	2.99	123.29	H-Bond (Protein Donor)	false
C3'	CG2	THR- 253	4.21	0	Hydrophobic	false
C5'	CG2	THR- 253	4.34	0	Hydrophobic	false
O5'	OD2	ASP- 257	2.69	133.48	H-Bond (Ligand Donor)	false
O5'	OD1	ASP- 257	3.41	157.41	H-Bond (Ligand Donor)	false