scPDB - 3lli entry

Protein Data Bank Entry:

PDB ID : 3lli

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sulfhydryl oxidase 1
ID:	QSOX1_HUMAN
AC:	O00391
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.8.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	47.077
Number of residues:	52
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.916	1069.875

% Hydrophobic	% Polar
45.74	54.26
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	64.84 %
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
-23.1739	11.7148	7.37326

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
C5'	CG	ARG- 401	4.34	0	Hydrophobic	false
O2P	CZ	ARG- 401	3.43	0	Ionic (Protein Cationic)	false
C1'	CB	PRO- 404	4.21	0	Hydrophobic	false
C3'	CB	PRO- 404	4.39	0	Hydrophobic	false
C5B	SG	CYS- 405	3.6	0	Hydrophobic	false
C8M	CD2	LEU- 407	4.44	0	Hydrophobic	false
C5B	CB	TRP- 408	4.31	0	Hydrophobic	false
C7M	CZ2	TRP- 408	4.1	0	Hydrophobic	false
C8M	CE2	TRP- 408	3.42	0	Hydrophobic	false
O2'	NE1	TRP- 408	3	160.98	H-Bond (Protein Donor)	false
C4B	CG2	VAL- 409	4.2	0	Hydrophobic	false
DuAr	DuAr	HIS- 412	3.92	0	Aromatic Face/Face	false
C7M	CG2	VAL- 443	4.23	0	Hydrophobic	false
C8M	CE2	PHE- 447	4	0	Hydrophobic	false
C1'	SG	CYS- 452	4.24	0	Hydrophobic	false
C6	CB	CYS- 452	3.73	0	Hydrophobic	false
C9A	CB	CYS- 452	3.58	0	Hydrophobic	false
C7M	CB	PHE- 456	3.39	0	Hydrophobic	false
N6A	O	TRP- 478	2.83	155.31	H-Bond (Ligand Donor)	false
O2A	NE2	HIS- 481	2.7	153.89	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 482	3.35	138.72	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 485	3.01	154.53	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 488	3.6	0	Hydrophobic	false
O2A	NZ	LYS- 500	3.42	0	Ionic (Protein Cationic)	false
O1P	NZ	LYS- 500	3.5	0	Ionic (Protein Cationic)	false
O4'	NZ	LYS- 500	2.91	134.92	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 500	2.73	146.36	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 500	3.5	138.86	H-Bond (Protein Donor)	false
C1B	CE2	TRP- 503	3.79	0	Hydrophobic	false