scPDB - 4j6d entry

Protein Data Bank Entry:

PDB ID : 4j6d

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-02-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytochrome P450 monooxygenase
ID:	Q5YNS8_NOCFA
AC:	Q5YNS8
Organism:	Nocardia farcinica
Reign:	Bacteria
TaxID:	247156
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.279
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.650	1063.125

% Hydrophobic	% Polar
61.90	38.10
According to VolSite

Ligand :

HET Code:	TES
Formula:	C19H28O2
Molecular weight:	288.424 g/mol
DrugBank ID:	DB00624
Buried Surface Area:	67.52 %
Polar Surface area:	37.29 Å2

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

Mass center Coordinates

X	Y	Z
-23.2872	29.8236	14.9471

Binding mode :

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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	CE	MET- 84	3.85	0	Hydrophobic	false
C19	CE	MET- 84	4.3	0	Hydrophobic	false
C11	CE	MET- 84	3.59	0	Hydrophobic	false
C2	CG1	VAL- 87	4.26	0	Hydrophobic	false
C6	CG	PHE- 92	3.8	0	Hydrophobic	false
C15	CE1	PHE- 92	4.38	0	Hydrophobic	false
C19	CE2	PHE- 92	4.18	0	Hydrophobic	false
C7	CE1	PHE- 92	3.95	0	Hydrophobic	false
C2	CZ	PHE- 179	3.47	0	Hydrophobic	false
C12	CE1	PHE- 180	3.94	0	Hydrophobic	false
C6	CB	ALA- 240	3.68	0	Hydrophobic	false
C1	CB	ALA- 243	3.78	0	Hydrophobic	false
C7	CB	ALA- 244	4.44	0	Hydrophobic	false
C15	CB	ALA- 244	3.92	0	Hydrophobic	false
C17	CG2	THR- 248	4	0	Hydrophobic	false
C16	CD2	LEU- 294	4.36	0	Hydrophobic	false
C18	CD2	LEU- 294	3.81	0	Hydrophobic	false
O17	OE1	GLN- 398	2.88	162.61	H-Bond (Ligand Donor)	false