scPDB - 2y46 entry

Protein Data Bank Entry:

PDB ID : 2y46

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 2011-01-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mycinamicin IV hydroxylase/epoxidase
ID:	MYCG_MICGR
AC:	Q59523
Organism:	Micromonospora griseorubida
Reign:	Bacteria
TaxID:	28040
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.434
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.362	2251.125

% Hydrophobic	% Polar
54.27	45.73
According to VolSite

Ligand :

HET Code:	MIV
Formula:	C37H62NO11
Molecular weight:	696.888 g/mol
DrugBank ID:	-
Buried Surface Area:	48.26 %
Polar Surface area:	143.65 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
25.3197	13.2647	92.5017

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
C18	CG	GLU- 77	3.87	0	Hydrophobic	false
C19	CB	GLU- 77	3.91	0	Hydrophobic	false
C37	CG1	VAL- 79	3.83	0	Hydrophobic	false
C10	CG2	VAL- 79	3.7	0	Hydrophobic	false
O10	O	GLY- 81	2.91	144.81	H-Bond (Ligand Donor)	false
C34	CB	LEU- 83	4.37	0	Hydrophobic	false
O10	N	LEU- 84	3.5	146.2	H-Bond (Protein Donor)	false
C31	CD2	LEU- 84	4.44	0	Hydrophobic	false
C32	CD2	LEU- 84	3.98	0	Hydrophobic	false
C35	CB	LEU- 84	3.85	0	Hydrophobic	false
C7	CD1	PHE- 168	3.6	0	Hydrophobic	false
C21	CB	SER- 170	3.82	0	Hydrophobic	false
C10	CE	MET- 179	4.43	0	Hydrophobic	false
C8	SD	MET- 179	3.57	0	Hydrophobic	false
C6	CE	MET- 179	3.94	0	Hydrophobic	false
C7	SD	MET- 179	3.85	0	Hydrophobic	false
C13	SD	MET- 179	4.08	0	Hydrophobic	false
C28	CB	VAL- 233	4.4	0	Hydrophobic	false
C29	CG2	VAL- 233	4.29	0	Hydrophobic	false
C30	CG2	VAL- 233	4.44	0	Hydrophobic	false
C34	CB	ALA- 234	3.98	0	Hydrophobic	false
C31	CB	ALA- 234	4.4	0	Hydrophobic	false
C32	CB	ALA- 234	4.15	0	Hydrophobic	false
C27	CG	GLU- 237	4.28	0	Hydrophobic	false
C35	CE1	PHE- 286	4.4	0	Hydrophobic	false
C31	CZ	PHE- 286	3.92	0	Hydrophobic	false
C32	CE2	PHE- 286	4.42	0	Hydrophobic	false
C25	CD1	LEU- 386	4.47	0	Hydrophobic	false
C27	CD1	LEU- 386	3.84	0	Hydrophobic	false
C27	CG	LEU- 387	4.17	0	Hydrophobic	false