scPDB - 2iyf entry

Protein Data Bank Entry:

PDB ID : 2iyf

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-07-17

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:	OLED_STRAT
AC:	Q53685
Organism:	Streptomyces antibioticus
Reign:	Bacteria
TaxID:	1890
EC Number:	2.4.1

Chains:

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

Ligand binding site composition:

B-Factor:	17.470
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	725.625

% Hydrophobic	% Polar
40.93	59.07
According to VolSite

Ligand :

HET Code:	ERY
Formula:	C37H68NO13
Molecular weight:	734.935 g/mol
DrugBank ID:	DB00199
Buried Surface Area:	47.11 %
Polar Surface area:	195.11 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-49.1442	-14.893	-15.515

Binding mode :

What is Poseview ?

2D View
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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- 19	2.6	154.35	H-Bond (Protein Donor)	false
C25	CD2	TRP- 73	3.81	0	Hydrophobic	false
C27	CB	TRP- 73	3.83	0	Hydrophobic	false
C32	CB	ASN- 80	4.26	0	Hydrophobic	false
C27	CB	ASN- 80	3.73	0	Hydrophobic	false
C32	CG1	VAL- 81	4.29	0	Hydrophobic	false
C7	CE1	PHE- 84	4.27	0	Hydrophobic	false
C8	CD1	PHE- 84	4.01	0	Hydrophobic	false
C33	CG	PHE- 84	3.66	0	Hydrophobic	false
C32	CE1	PHE- 84	4.15	0	Hydrophobic	false
C35	CD1	ILE- 111	3.69	0	Hydrophobic	false
C31	CD1	ILE- 111	4.05	0	Hydrophobic	false
C33	CG2	THR- 112	4.41	0	Hydrophobic	false
C34	CE1	TYR- 114	4.29	0	Hydrophobic	false
C33	CZ	TYR- 114	4.35	0	Hydrophobic	false
C30	CG	LEU- 134	4.25	0	Hydrophobic	false
C37	CD1	LEU- 134	3.71	0	Hydrophobic	false
C37	CZ	TYR- 140	3.8	0	Hydrophobic	false
C34	CB	ALA- 182	3.71	0	Hydrophobic	false
O13	OG	SER- 183	2.88	153.75	H-Bond (Protein Donor)	false
C19	CB	ASP- 329	3.96	0	Hydrophobic	false