scPDB - 4pv5 entry

Protein Data Bank Entry:

PDB ID : 4pv5

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-03-15

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	58 %
B	42 %

Ligand binding site composition:

B-Factor:	29.992
Number of residues:	24
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.158	752.625

% Hydrophobic	% Polar
65.47	34.53
According to VolSite

Ligand :

HET Code:	CBW
Formula:	C30H45O4
Molecular weight:	469.676 g/mol
DrugBank ID:	DB13089
Buried Surface Area:	38.93 %
Polar Surface area:	77.43 Å2

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

Mass center Coordinates

X	Y	Z
12.2464	4.93409	24.2248

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
C22	CE	MET- 36	4.08	0	Hydrophobic	false
O35	CZ	ARG- 38	3.59	0	Ionic (Protein Cationic)	false
O35	NE	ARG- 38	2.68	167.88	H-Bond (Protein Donor)	false
C27	CE	MET- 66	3.73	0	Hydrophobic	false
C16	CZ	PHE- 68	3.99	0	Hydrophobic	false
C34	CD2	PHE- 68	4.08	0	Hydrophobic	false
C34	CG2	THR- 102	4.28	0	Hydrophobic	false
C22	CG2	THR- 102	3.87	0	Hydrophobic	false
O35	ND2	ASN- 104	3.47	166.19	H-Bond (Protein Donor)	false
O34	CZ	ARG- 123	3.97	0	Ionic (Protein Cationic)	false
O35	CZ	ARG- 123	3.78	0	Ionic (Protein Cationic)	false
C19	CG1	VAL- 150	4.47	0	Hydrophobic	false
C19	CB	LYS- 151	4.27	0	Hydrophobic	false
C24	CD	LYS- 151	3.55	0	Hydrophobic	false
C24	CB	ASP- 155	3.98	0	Hydrophobic	false
C26	CE2	PHE- 163	3.78	0	Hydrophobic	false
C28	CZ	PHE- 163	4.36	0	Hydrophobic	false