scPDB - 3gya entry

Protein Data Bank Entry:

PDB ID : 3gya

Resolution :1.620 Å

Experimental Method : X-ray

Deposition Date : 2009-04-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GCN5-related N-acetyltransferase
ID:	B1YEL6_EXIS2
AC:	B1YEL6
Organism:	Exiguobacterium sibiricum
Reign:	Bacteria
TaxID:	262543
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.556
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.408	621.000

% Hydrophobic	% Polar
46.20	53.80
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	42.27 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
19.1258	15.1179	1.34923

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
C6P	CZ	PHE- 28	3.87	0	Hydrophobic	false
CDP	CG1	VAL- 81	3.97	0	Hydrophobic	false
CDP	CG2	VAL- 83	3.97	0	Hydrophobic	false
CAP	CB	VAL- 83	4.05	0	Hydrophobic	false
O9P	N	VAL- 83	3.06	157.84	H-Bond (Protein Donor)	false
CAP	CG	ARG- 88	3.95	0	Hydrophobic	false
N6A	OG	SER- 89	3.47	157.53	H-Bond (Ligand Donor)	false
N7A	OG	SER- 89	2.75	156.12	H-Bond (Protein Donor)	false
O5A	N	SER- 89	2.94	164.34	H-Bond (Protein Donor)	false
O2A	N	GLY- 91	2.79	153.77	H-Bond (Protein Donor)	false
O4A	N	GLY- 93	2.81	158.74	H-Bond (Protein Donor)	false
O1A	OG1	THR- 94	2.67	159.44	H-Bond (Protein Donor)	false
O1A	N	THR- 94	3.01	145.9	H-Bond (Protein Donor)	false
CEP	CB	ALA- 118	3.72	0	Hydrophobic	false
C1B	CB	PHE- 121	4.07	0	Hydrophobic	false
CCP	CD1	PHE- 121	3.9	0	Hydrophobic	false
CDP	CE2	PHE- 121	3.99	0	Hydrophobic	false
C4B	CD1	PHE- 121	3.61	0	Hydrophobic	false
CEP	CD2	PHE- 121	4.05	0	Hydrophobic	false
O4A	O	HOH- 155	2.61	167.02	H-Bond (Protein Donor)	false