scPDB - 3w0u entry

Protein Data Bank Entry:

PDB ID : 3w0u

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2012-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lactoylglutathione lyase
ID:	LGUL_HUMAN
AC:	Q04760
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.4.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	17.760
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.349	634.500

% Hydrophobic	% Polar
61.17	38.83
According to VolSite

Ligand :

HET Code:	HPW
Formula:	C19H18N3O6S2
Molecular weight:	448.493 g/mol
DrugBank ID:	-
Buried Surface Area:	64.04 %
Polar Surface area:	152.46 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
9.8263	-11.6449	-28.7403

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
O25	NE2	GLN- 33	2.96	153.89	H-Bond (Protein Donor)	false
C32	SG	CYS- 60	3.72	0	Hydrophobic	false
C14	CD1	PHE- 67	3.38	0	Hydrophobic	false
C17	CD1	LEU- 69	4.31	0	Hydrophobic	false
C26	CD1	LEU- 69	3.67	0	Hydrophobic	false
C32	CG2	ILE- 88	4.37	0	Hydrophobic	false
C26	CD1	LEU- 92	4.49	0	Hydrophobic	false
C14	CG2	THR- 101	3.83	0	Hydrophobic	false
C1	CD	LYS- 150	4.46	0	Hydrophobic	false
C1	CG	MET- 157	3.77	0	Hydrophobic	false
C30	CE	MET- 157	3.56	0	Hydrophobic	false
C1	CD2	LEU- 160	3.61	0	Hydrophobic	false
C8	CD1	LEU- 160	3.91	0	Hydrophobic	false
C20	CD1	LEU- 160	3.93	0	Hydrophobic	false
C31	CB	MET- 179	4.33	0	Hydrophobic	false
C28	CE	MET- 179	3.4	0	Hydrophobic	false
C28	CE	MET- 179	3.4	0	Hydrophobic	false
C30	CD1	LEU- 182	4.2	0	Hydrophobic	false
O22	ZN	ZN- 202	2.2	0	Metal Acceptor	false
O25	ZN	ZN- 202	2.33	0	Metal Acceptor	false
O15	O	HOH- 308	2.66	179.94	H-Bond (Protein Donor)	false
N11	O	HOH- 409	2.76	134.91	H-Bond (Ligand Donor)	false