scPDB - 2iya entry

Protein Data Bank Entry:

PDB ID : 2iya

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oleandomycin glycosyltransferase
ID:	Q3HTL7_STRAT
AC:	Q3HTL7
Organism:	Streptomyces antibioticus
Reign:	Bacteria
TaxID:	1890
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	12.563
Number of residues:	47
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.704	1795.500

% Hydrophobic	% Polar
53.95	46.05
According to VolSite

Ligand :

HET Code:	ZIO
Formula:	C35H62NO12
Molecular weight:	688.866 g/mol
DrugBank ID:	-
Buried Surface Area:	71.37 %
Polar Surface area:	167.17 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
20.8419	43.5395	63.04

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
O8	NE2	HIS- 25	2.72	168.58	H-Bond (Protein Donor)	false
C25	CE3	TRP- 79	3.94	0	Hydrophobic	false
C27	CG	PRO- 80	4.44	0	Hydrophobic	false
O11	NE2	GLN- 83	2.74	158.47	H-Bond (Protein Donor)	false
C32	CG	GLN- 83	4.3	0	Hydrophobic	false
C14	CG	GLN- 83	4.19	0	Hydrophobic	false
C21	CB	GLN- 83	4.05	0	Hydrophobic	false
C32	CB	ALA- 86	3.52	0	Hydrophobic	false
C27	CB	ALA- 86	3.53	0	Hydrophobic	false
C34	SD	MET- 87	4.16	0	Hydrophobic	false
C33	CG	MET- 87	4.22	0	Hydrophobic	false
C7	CE2	PHE- 90	4.06	0	Hydrophobic	false
C32	CE2	PHE- 90	4.16	0	Hydrophobic	false
C33	CD2	PHE- 90	3.29	0	Hydrophobic	false
C4	CD1	ILE- 117	4.29	0	Hydrophobic	false
C35	CB	ILE- 117	4.08	0	Hydrophobic	false
C33	CZ2	TRP- 120	3.38	0	Hydrophobic	false
C31	CG2	THR- 139	4.09	0	Hydrophobic	false
C30	CG2	THR- 139	3.66	0	Hydrophobic	false
C30	CZ	PHE- 140	3.63	0	Hydrophobic	false
C20	CZ	PHE- 140	4.39	0	Hydrophobic	false
C36	CB	ALA- 142	4.31	0	Hydrophobic	false
C13	CZ	PHE- 146	3.77	0	Hydrophobic	false
C15	CG1	VAL- 150	3.93	0	Hydrophobic	false
C20	CG2	VAL- 150	4.23	0	Hydrophobic	false
C34	CB	LEU- 207	3.42	0	Hydrophobic	false
C12	CG2	ILE- 208	4.15	0	Hydrophobic	false
C25	CZ	PHE- 266	4.07	0	Hydrophobic	false
C26	CD1	ILE- 350	4.38	0	Hydrophobic	false
C21	CD1	ILE- 350	4.19	0	Hydrophobic	false
C20	CB	ALA- 351	3.76	0	Hydrophobic	false
C17	CB	ALA- 351	4.11	0	Hydrophobic	false
C30	CG	GLU- 352	3.76	0	Hydrophobic	false
C31	CG	GLU- 352	4.05	0	Hydrophobic	false
C16	CB	GLU- 352	4.09	0	Hydrophobic	false
O6	N	GLU- 352	2.99	146.12	H-Bond (Protein Donor)	false
C20	SD	MET- 355	3.55	0	Hydrophobic	false