scPDB - 3t4n entry

Protein Data Bank Entry:

PDB ID : 3t4n

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-07-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5'-AMP-activated protein kinase subunit gamma
ID:	AAKG_YEAST
AC:	P12904
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.743
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.955	529.875

% Hydrophobic	% Polar
43.95	56.05
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	54.94 %
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
-26.7447	68.223	-2.98274

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
O1B	NE2	GLN- 168	3.28	155.03	H-Bond (Protein Donor)	false
O2'	OG1	THR- 196	2.67	165.13	H-Bond (Protein Donor)	false
C2'	CG2	THR- 196	3.99	0	Hydrophobic	false
N6	O	LYS- 201	3.08	170.87	H-Bond (Ligand Donor)	false
N1	N	LYS- 201	2.93	158.45	H-Bond (Protein Donor)	false
O1A	N	SER- 222	3.31	162.37	H-Bond (Protein Donor)	false
O2A	OG	SER- 222	3.22	162.47	H-Bond (Protein Donor)	false
N6	O	SER- 223	3.1	140.56	H-Bond (Ligand Donor)	false
C2'	CG1	VAL- 308	4.39	0	Hydrophobic	false
O1B	OG1	THR- 310	3.34	144.22	H-Bond (Protein Donor)	false
C2'	CG2	THR- 310	3.64	0	Hydrophobic	false
O1B	N	SER- 312	3	156.42	H-Bond (Protein Donor)	false
O1B	OG	SER- 312	2.63	157.67	H-Bond (Protein Donor)	false
O2B	OG	SER- 312	3.02	124.74	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 313	2.65	168.31	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 313	2.55	144.3	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 313	3.49	157.23	H-Bond (Ligand Donor)	false
O1B	O	HOH- 406	2.59	126.33	H-Bond (Protein Donor)	false