scPDB - 2ya3 entry

Protein Data Bank Entry:

PDB ID : 2ya3

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-02-17

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-1
ID:	AAKG1_RAT
AC:	P80385
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.443
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.969	1552.500

% Hydrophobic	% Polar
42.61	57.39
According to VolSite

Ligand :

HET Code:	J7V
Formula:	C24H26N7O12P2
Molecular weight:	666.450 g/mol
DrugBank ID:	-
Buried Surface Area:	62.48 %
Polar Surface area:	299.12 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
7.14133	10.3369	29.9124

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
OAI	OG1	THR- 86	2.89	150.41	H-Bond (Protein Donor)	false
CBL	CG2	THR- 86	4.18	0	Hydrophobic	false
OAI	N	THR- 88	2.99	146.29	H-Bond (Protein Donor)	false
CAT	CB	THR- 88	4.08	0	Hydrophobic	false
CBM	CG2	THR- 88	4.46	0	Hydrophobic	false
OAH	OD2	ASP- 89	2.8	170.51	H-Bond (Ligand Donor)	false
OAH	OD1	ASP- 89	3.14	129.11	H-Bond (Ligand Donor)	false
OAE	ND2	ASN- 92	3.3	121.77	H-Bond (Protein Donor)	false
CAP	CB	ASN- 92	4.12	0	Hydrophobic	false
CAA	CG	ARG- 96	3.99	0	Hydrophobic	false
CAA	CH2	TRP- 116	3.71	0	Hydrophobic	false
CAS	CB	TYR- 120	4.11	0	Hydrophobic	false
CAA	CB	TYR- 120	3.89	0	Hydrophobic	false
CBE	CB	TYR- 120	3.23	0	Hydrophobic	false
CAN	CG	LEU- 121	3.74	0	Hydrophobic	false
OAD	NZ	LYS- 126	2.78	172.5	H-Bond (Protein Donor)	false
N6	O	VAL- 129	2.81	172.61	H-Bond (Ligand Donor)	false
N1	N	VAL- 129	2.91	169.47	H-Bond (Protein Donor)	false
CBO	CD1	ILE- 149	3.84	0	Hydrophobic	false
CAT	CD1	ILE- 149	4.14	0	Hydrophobic	false
OAK	N	HIS- 150	2.76	167.42	H-Bond (Protein Donor)	false
OAF	NH2	ARG- 151	3.45	131.77	H-Bond (Protein Donor)	false
OAF	NE	ARG- 151	3.07	146.25	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 151	3.68	0	Ionic (Protein Cationic)	false
N6	O	ARG- 151	2.92	159.35	H-Bond (Ligand Donor)	false
OAI	NZ	LYS- 242	3.52	0	Ionic (Protein Cationic)	false