scPDB - 4jl5 entry

Protein Data Bank Entry:

PDB ID : 4jl5

Resolution :1.240 Å

Experimental Method : X-ray

Deposition Date : 2013-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate kinase
ID:	KAD_AQUAE
AC:	O66490
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.842
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	ADP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.996	955.125

% Hydrophobic	% Polar
44.52	55.48
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.08 %
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
-23.1841	2.41293	14.6763

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
O3B	N	GLY- 10	2.88	161.46	H-Bond (Protein Donor)	false
O1B	N	GLY- 12	3.01	130.01	H-Bond (Protein Donor)	false
O3A	N	GLY- 12	3.05	133.46	H-Bond (Protein Donor)	false
O1B	N	LYS- 13	2.85	155.87	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 13	2.77	161.09	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 13	2.77	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 14	2.85	158.12	H-Bond (Protein Donor)	false
O2A	N	THR- 15	2.92	146.82	H-Bond (Protein Donor)	false
O2A	OG1	THR- 15	2.68	155.03	H-Bond (Protein Donor)	false
C1'	CD	ARG- 120	4.23	0	Hydrophobic	false
C4'	CB	ARG- 120	3.98	0	Hydrophobic	false
DuAr	CZ	ARG- 120	3.59	17.12	Pi/Cation	false
O3B	NH1	ARG- 124	3.26	130.41	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 124	2.82	146.72	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 124	3.95	0	Ionic (Protein Cationic)	false
C3'	CD	ARG- 124	3.77	0	Hydrophobic	false
C3'	CG1	VAL- 133	3.52	0	Hydrophobic	false
O3'	O	TYR- 134	2.83	135.87	H-Bond (Ligand Donor)	false
O2'	O	TYR- 134	3.41	141.7	H-Bond (Ligand Donor)	false
C1'	CB	HIS- 135	4.19	0	Hydrophobic	false
N6	O	LYS- 189	2.87	154.12	H-Bond (Ligand Donor)	false