scPDB - 4kyh entry

Protein Data Bank Entry:

PDB ID : 4kyh

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2013-05-29

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_MOUSE
AC:	Q9CPU0
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	4.4.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	14.988
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.910	475.875

% Hydrophobic	% Polar
68.09	31.91
According to VolSite

Ligand :

HET Code:	ZST
Formula:	C19H11F3N3O3S
Molecular weight:	418.369 g/mol
DrugBank ID:	DB08772
Buried Surface Area:	38.69 %
Polar Surface area:	113.93 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-3.86934	16.0671	-0.0487586

Binding mode :

What is Poseview ?

2D View
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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
C7	CE	MET- 36	3.53	0	Hydrophobic	false
O2	CZ	ARG- 38	3.77	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 38	3.72	0	Ionic (Protein Cationic)	false
O2	NH2	ARG- 38	3.16	131.58	H-Bond (Protein Donor)	false
O3	NE	ARG- 38	2.83	140.75	H-Bond (Protein Donor)	false
C9	SD	MET- 66	4.15	0	Hydrophobic	false
C9	CE2	PHE- 68	4.42	0	Hydrophobic	false
C17	CD2	PHE- 68	4.06	0	Hydrophobic	false
C7	CD2	LEU- 70	3.73	0	Hydrophobic	false
C17	CG2	THR- 102	4.18	0	Hydrophobic	false
C8	CG2	THR- 102	3.56	0	Hydrophobic	false
O3	ND2	ASN- 104	3.08	169.49	H-Bond (Protein Donor)	false
F1	CG1	VAL- 150	4.04	0	Hydrophobic	false
F2	CG1	VAL- 150	4.25	0	Hydrophobic	false
F1	CB	LYS- 151	3.54	0	Hydrophobic	false