scPDB - 3td7 entry

Protein Data Bank Entry:

PDB ID : 3td7

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2011-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable FAD-linked sulfhydryl oxidase R596
ID:	YR596_MIMIV
AC:	Q5UP54
Organism:	Acanthamoeba polyphaga mimivirus
Reign:	Viruses
TaxID:	212035
EC Number:	1.8.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	36.660
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.024	351.000

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	65.69 %
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
5.22187	-47.381	6.12238

Binding mode :

What is Poseview ?

2D View
3D View

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
C1'	CB	THR- 37	4.4	0	Hydrophobic	false
C5'	CG	LYS- 38	4.21	0	Hydrophobic	false
C8M	CZ3	TRP- 40	4.14	0	Hydrophobic	false
O2A	OG1	THR- 42	2.59	170.89	H-Bond (Protein Donor)	false
C7M	CH2	TRP- 45	3.9	0	Hydrophobic	false
C8	CE2	TRP- 45	3.47	0	Hydrophobic	false
O2'	NE1	TRP- 45	2.87	164.53	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 78	3.79	0	Hydrophobic	false
C7M	CD1	TYR- 87	4.12	0	Hydrophobic	false
N6A	O	TYR- 114	3.44	145.83	H-Bond (Ligand Donor)	false
DuAr	DuAr	HIS- 117	3.59	0	Aromatic Face/Face	false
N6A	OD1	ASN- 118	3.02	127.25	H-Bond (Ligand Donor)	false
C6	CG2	VAL- 120	4.11	0	Hydrophobic	false
C9A	CG1	VAL- 120	4.36	0	Hydrophobic	false
C2'	CG1	VAL- 120	4.45	0	Hydrophobic	false
N7A	ND2	ASN- 121	3.12	150.09	H-Bond (Protein Donor)	false
O4	NZ	LYS- 123	2.74	164.72	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 124	3.99	0	Hydrophobic	false
O1P	OH	TYR- 128	3.1	139.33	H-Bond (Protein Donor)	false
C5B	CE2	TYR- 128	3.8	0	Hydrophobic	false
C3B	CD2	TYR- 128	4.03	0	Hydrophobic	false
C2B	CD1	LEU- 130	3.44	0	Hydrophobic	false
C5B	CE	MET- 173	4.43	0	Hydrophobic	false
O3B	N	ASP- 174	2.83	152.02	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 174	2.72	165.98	H-Bond (Ligand Donor)	false
C2B	CB	ASP- 174	3.7	0	Hydrophobic	false
O2P	CZ	ARG- 237	3.5	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 237	2.86	159.52	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 237	3.27	136.18	H-Bond (Protein Donor)	false
O1A	O	HOH- 299	2.65	179.96	H-Bond (Protein Donor)	false