scPDB - 4x8l entry

Protein Data Bank Entry:

PDB ID : 4x8l

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2014-12-10

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_ECOLI
AC:	P69441
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.283
Number of residues:	67
Including
Standard Amino Acids:	61
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.180	256.500

% Hydrophobic	% Polar
51.32	48.68
According to VolSite

Ligand :

HET Code:	AP5
Formula:	C20H24N10O22P5
Molecular weight:	911.327 g/mol
DrugBank ID:	DB01717
Buried Surface Area:	78.63 %
Polar Surface area:	543.69 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
19.3111	15.1504	74.7915

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	3.07	141.78	H-Bond (Protein Donor)	false
O3G	N	GLY- 10	3.37	142.68	H-Bond (Protein Donor)	false
O3A	N	GLY- 12	2.97	126.01	H-Bond (Protein Donor)	false
O1B	N	GLY- 12	3.23	147.15	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 13	2.72	166.01	H-Bond (Protein Donor)	false
O1B	N	LYS- 13	3	154.64	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 13	2.72	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 13	3.34	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 14	2.78	159.98	H-Bond (Protein Donor)	false
O1A	N	THR- 15	2.92	142.89	H-Bond (Protein Donor)	false
O1A	OG1	THR- 15	2.67	158.29	H-Bond (Protein Donor)	false
N7B	OG1	THR- 31	2.92	157.59	H-Bond (Protein Donor)	false
C1J	CD1	LEU- 35	3.88	0	Hydrophobic	false
O2E	NH1	ARG- 36	3.43	134.2	H-Bond (Protein Donor)	false
O2E	NH2	ARG- 36	2.89	164.93	H-Bond (Protein Donor)	false
O2E	CZ	ARG- 36	3.61	0	Ionic (Protein Cationic)	false
C4J	CG	MET- 53	3.99	0	Hydrophobic	false
C1J	CG	MET- 53	4	0	Hydrophobic	false
C2J	CD2	LEU- 58	4.19	0	Hydrophobic	false
N3B	N	VAL- 59	3.17	147.12	H-Bond (Protein Donor)	false
C1J	CG1	VAL- 59	4.2	0	Hydrophobic	false
N6B	O	GLY- 85	3.02	127.57	H-Bond (Ligand Donor)	false
O2D	CZ	ARG- 88	3.76	0	Ionic (Protein Cationic)	false
O1E	CZ	ARG- 88	3.68	0	Ionic (Protein Cationic)	false
O1E	NH1	ARG- 88	2.91	147.78	H-Bond (Protein Donor)	false
O5J	NH2	ARG- 88	3.32	152.45	H-Bond (Protein Donor)	false
N6B	OE1	GLN- 92	2.91	164.82	H-Bond (Ligand Donor)	false
N1B	NE2	GLN- 92	3.08	153.75	H-Bond (Protein Donor)	false
C5F	CD	ARG- 119	4.32	0	Hydrophobic	false
C4F	CG	ARG- 119	3.98	0	Hydrophobic	false
C1F	CD	ARG- 119	4.41	0	Hydrophobic	false
DuAr	CZ	ARG- 119	3.66	8.45	Pi/Cation	false
C5F	CD1	ILE- 120	3.75	0	Hydrophobic	false
O2A	NH1	ARG- 123	2.97	147.03	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 123	3.21	136.08	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 123	3.23	124.58	H-Bond (Protein Donor)	false
O1D	NH2	ARG- 123	3.48	161.67	H-Bond (Protein Donor)	false
C3F	CD	ARG- 123	3.82	0	Hydrophobic	false
C3F	CG2	VAL- 132	3.89	0	Hydrophobic	false
O3F	O	TYR- 133	2.8	153.36	H-Bond (Ligand Donor)	false
C1F	CB	HIS- 134	3.85	0	Hydrophobic	false
O2G	NH1	ARG- 156	3.11	151.36	H-Bond (Protein Donor)	false
O1D	NH2	ARG- 156	3.3	130.71	H-Bond (Protein Donor)	false
O3D	NH1	ARG- 156	3.36	140.1	H-Bond (Protein Donor)	false
O3D	NH2	ARG- 156	3.04	158.67	H-Bond (Protein Donor)	false
O1D	CZ	ARG- 167	3.07	0	Ionic (Protein Cationic)	false
C5J	CD	ARG- 167	4.19	0	Hydrophobic	false
C3J	CD	ARG- 167	4.21	0	Hydrophobic	false
N6A	O	LYS- 200	2.66	161.24	H-Bond (Ligand Donor)	false
O2B	MG	MG- 302	2.49	0	Metal Acceptor	false
O3J	O	HOH- 536	2.81	160.08	H-Bond (Ligand Donor)	false
O2F	O	HOH- 545	2.61	152.89	H-Bond (Protein Donor)	false
N6A	O	HOH- 603	3.35	122.95	H-Bond (Ligand Donor)	false
O1E	O	HOH- 636	3.05	135.82	H-Bond (Protein Donor)	false