scPDB - 2yiu entry

Protein Data Bank Entry:

PDB ID : 2yiu

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-05-16

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_PARDE
AC:	P05418
Organism:	Paracoccus denitrificans
Reign:	Bacteria
TaxID:	266
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	87 %
F	13 %

Ligand binding site composition:

B-Factor:	18.203
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.926	793.125

% Hydrophobic	% Polar
78.30	21.70
According to VolSite

Ligand :

HET Code:	SMA
Formula:	C30H42O7
Molecular weight:	514.650 g/mol
DrugBank ID:	-
Buried Surface Area:	68.94 %
Polar Surface area:	83.45 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
1.35481	-39.9279	-38.0692

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
C25	CD2	LEU- 137	3.51	0	Hydrophobic	false
C22	SD	MET- 140	4.04	0	Hydrophobic	false
C23	CE	MET- 140	4.28	0	Hydrophobic	false
C25	CB	MET- 140	4.42	0	Hydrophobic	false
C24	CB	PHE- 144	3.86	0	Hydrophobic	false
C26	CE2	PHE- 144	3.9	0	Hydrophobic	false
C21	SD	MET- 145	4.22	0	Hydrophobic	false
C5M	SG	CYS- 154	3.63	0	Hydrophobic	false
C7M	SD	MET- 154	4	0	Hydrophobic	false
O4	NE2	HIS- 155	2.85	162.95	H-Bond (Protein Donor)	false
C5M	CG2	VAL- 161	4.03	0	Hydrophobic	false
C5	CG1	VAL- 161	3.64	0	Hydrophobic	false
C8	CD1	ILE- 162	4.28	0	Hydrophobic	false
C10	CG1	ILE- 162	4.42	0	Hydrophobic	false
C13	CG2	ILE- 162	4.15	0	Hydrophobic	false
C26	CE1	PHE- 166	3.77	0	Hydrophobic	false
C21	CD2	LEU- 180	3.75	0	Hydrophobic	false
C26	CD1	LEU- 180	3.76	0	Hydrophobic	false
C21	CE1	PHE- 194	3.54	0	Hydrophobic	false
C5M	CG1	ILE- 292	4.1	0	Hydrophobic	false
C7M	CD1	ILE- 292	3.51	0	Hydrophobic	false
C8	CB	PRO- 294	3.71	0	Hydrophobic	false
C6	CG	PRO- 294	3.85	0	Hydrophobic	false
O8	OE2	GLU- 295	3.14	120.82	H-Bond (Ligand Donor)	false
C9	CB	PHE- 298	3.73	0	Hydrophobic	false
C10	CG	PHE- 298	4.45	0	Hydrophobic	false
C24	CZ	PHE- 298	4.08	0	Hydrophobic	false
C22	CD1	PHE- 298	3.56	0	Hydrophobic	false
C22	CB	PHE- 301	3.87	0	Hydrophobic	false
C3M	CD1	TYR- 302	3.86	0	Hydrophobic	false
C5M	CE1	TYR- 302	4.42	0	Hydrophobic	false
C3M	CB	LEU- 305	4.43	0	Hydrophobic	false
C3M	SD	MET- 336	3.68	0	Hydrophobic	false
C10	SD	MET- 336	4.44	0	Hydrophobic	false
C23	CE	MET- 336	4.04	0	Hydrophobic	false
C14	CE1	PHE- 337	4.14	0	Hydrophobic	false
C23	CE1	PHE- 337	3.45	0	Hydrophobic	false
C25	CE1	PHE- 337	4.39	0	Hydrophobic	false
C23	CD1	ILE- 340	3.73	0	Hydrophobic	false