scPDB - 1ppj entry

Protein Data Bank Entry:

PDB ID : 1ppj

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-06-16

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_BOVIN
AC:	P00157
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.138
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.744	1005.750

% Hydrophobic	% Polar
69.46	30.54
According to VolSite

Ligand :

HET Code:	ANY
Formula:	C29H42N2O9
Molecular weight:	562.652 g/mol
DrugBank ID:	-
Buried Surface Area:	48.07 %
Polar Surface area:	157.32 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
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
55.31	101.449	82.0525

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
C18	CB	ALA- 17	4.47	0	Hydrophobic	false
C3	CD1	ILE- 27	3.48	0	Hydrophobic	false
C3	CB	TRP- 31	4.45	0	Hydrophobic	false
C25	CD2	LEU- 41	3.91	0	Hydrophobic	false
C25	CG1	ILE- 42	4.43	0	Hydrophobic	false
C22	CG	MET- 190	4.03	0	Hydrophobic	false
C23	CG	MET- 194	4.5	0	Hydrophobic	false
C13	CD1	LEU- 197	4.24	0	Hydrophobic	false
C12	CD1	LEU- 197	3.42	0	Hydrophobic	false
C26	CZ	PHE- 220	3.85	0	Hydrophobic	false
C1	CE1	PHE- 220	3.34	0	Hydrophobic	false
N1	OD1	ASP- 228	2.79	141.42	H-Bond (Ligand Donor)	false
O1	OD1	ASP- 228	3.39	161.07	H-Bond (Ligand Donor)	false
O2	O	HOH- 4027	2.59	164.11	H-Bond (Protein Donor)	false