scPDB - 2ibz entry

Protein Data Bank Entry:

PDB ID : 2ibz

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-09-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome b
ID:	CYB_YEAST
AC:	P00163
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	95 %
E	5 %

Ligand binding site composition:

B-Factor:	34.490
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.974	452.250

% Hydrophobic	% Polar
55.97	44.03
According to VolSite

Ligand :

HET Code:	UQ6
Formula:	C39H60O4
Molecular weight:	592.891 g/mol
DrugBank ID:	-
Buried Surface Area:	36.37 %
Polar Surface area:	58.92 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-9.63323	54.458	4.9104

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
C1M	CB	TYR- 16	4.43	0	Hydrophobic	false
C1M	CG1	ILE- 17	4.35	0	Hydrophobic	false
C10	CG1	ILE- 17	4.42	0	Hydrophobic	false
C4M	CD1	ILE- 26	4.26	0	Hydrophobic	false
C16	CD2	LEU- 40	4.31	0	Hydrophobic	false
C20	CG	LEU- 40	4.5	0	Hydrophobic	false
C20	CG2	VAL- 41	4.08	0	Hydrophobic	false
C20	CD1	ILE- 44	3.28	0	Hydrophobic	false
C27	CG2	ILE- 44	4.46	0	Hydrophobic	false
C27	CG2	VAL- 45	4.16	0	Hydrophobic	false
C27	CD1	ILE- 48	4.32	0	Hydrophobic	false
C32	CZ	PHE- 49	3.98	0	Hydrophobic	false
C35	CZ	PHE- 49	4.29	0	Hydrophobic	false
C36	CE	MET- 82	4.3	0	Hydrophobic	false
C25	CE2	PHE- 188	4.37	0	Hydrophobic	false
C1M	CD2	LEU- 198	4.24	0	Hydrophobic	false
C12	CD1	LEU- 198	4.08	0	Hydrophobic	false
C15	CD1	LEU- 198	4.32	0	Hydrophobic	false
C3M	CD2	LEU- 201	3.7	0	Hydrophobic	false
C3M	CB	SER- 206	4.42	0	Hydrophobic	false
C3M	CE	MET- 221	4.4	0	Hydrophobic	false
C4M	SD	MET- 221	4.07	0	Hydrophobic	false
O5	O	HOH- 516	3.13	144.71	H-Bond (Protein Donor)	false
O2	O	HOH- 521	3.46	143.1	H-Bond (Protein Donor)	false