scPDB - 4e0i entry

Protein Data Bank Entry:

PDB ID : 4e0i

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-03-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mitochondrial FAD-linked sulfhydryl oxidase ERV1
ID:	ERV1_YEAST
AC:	P27882
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.8.3.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	80 %
B	8 %
C	12 %

Ligand binding site composition:

B-Factor:	43.256
Number of residues:	50
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.170	1383.750

% Hydrophobic	% Polar
57.07	42.93
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	65.63 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-11.1993	-10.434	15.9932

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
C2B	CD1	TYR- 79	3.62	0	Hydrophobic	false
O4'	OE2	GLU- 88	3.08	139.75	H-Bond (Ligand Donor)	false
C5'	CB	GLU- 88	4.28	0	Hydrophobic	false
C5B	CB	ARG- 92	4.33	0	Hydrophobic	false
C5'	CB	ARG- 92	4.18	0	Hydrophobic	false
O2P	NE	ARG- 92	2.97	151.27	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 92	3.02	145.13	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 92	3.43	0	Ionic (Protein Cationic)	false
C8M	CB	SER- 94	3.6	0	Hydrophobic	false
C7M	CZ2	TRP- 95	4.02	0	Hydrophobic	false
C8M	CE2	TRP- 95	3.4	0	Hydrophobic	false
O2'	NE1	TRP- 95	2.88	169.84	H-Bond (Protein Donor)	false
C8M	CD1	LEU- 98	4.11	0	Hydrophobic	false
C7M	CE2	PHE- 124	4.14	0	Hydrophobic	false
C8M	CZ	TYR- 128	4.08	0	Hydrophobic	false
C7M	CD2	PHE- 137	3.87	0	Hydrophobic	false
N6A	O	CYS- 159	2.95	151.89	H-Bond (Ligand Donor)	false
O2A	NE2	HIS- 162	3.38	172.41	H-Bond (Protein Donor)	false
C6	CG2	VAL- 165	4.22	0	Hydrophobic	false
C9A	CG1	VAL- 165	4.38	0	Hydrophobic	false
C2'	CG1	VAL- 165	4.12	0	Hydrophobic	false
N7A	ND2	ASN- 166	3.15	166.38	H-Bond (Protein Donor)	false
O4	NZ	LYS- 168	2.98	156.16	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 169	3.81	0	Hydrophobic	false
O1P	NZ	LYS- 171	3.71	0	Ionic (Protein Cationic)	false
DuAr	DuAr	PHE- 174	3.77	0	Aromatic Face/Face	false
C2B	CE2	PHE- 174	4.45	0	Hydrophobic	false
O2B	NE	ARG- 182	2.91	167.87	H-Bond (Protein Donor)	false
C4B	CZ2	TRP- 183	4.2	0	Hydrophobic	false
C1B	CZ2	TRP- 183	3.82	0	Hydrophobic	false
N3A	NE1	TRP- 183	3.04	175.86	H-Bond (Protein Donor)	false