scPDB - 1bh5 entry

Protein Data Bank Entry:

PDB ID : 1bh5

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1998-06-13

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	12 %
C	41 %
D	46 %

Ligand binding site composition:

B-Factor:	15.119
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.108	867.375

% Hydrophobic	% Polar
45.91	54.09
According to VolSite

Ligand :

HET Code:	GTX
Formula:	C16H28N3O6S
Molecular weight:	390.475 g/mol
DrugBank ID:	-
Buried Surface Area:	58.1 %
Polar Surface area:	191.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
32.9182	-9.15569	119.815

Binding mode :

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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
O31	OG	SER- 17	3.01	127.6	H-Bond (Protein Donor)	false
O32	OG	SER- 17	2.6	166.13	H-Bond (Protein Donor)	false
O11	CZ	ARG- 37	3.82	0	Ionic (Protein Cationic)	false
O12	CZ	ARG- 37	3.61	0	Ionic (Protein Cationic)	false
O11	NE	ARG- 37	2.82	153.37	H-Bond (Protein Donor)	false
O12	NH2	ARG- 37	3.19	127.41	H-Bond (Protein Donor)	false
O12	NE	ARG- 37	3.35	125.82	H-Bond (Protein Donor)	false
C6S	SG	CYS- 60	3.21	0	Hydrophobic	false
C2S	CZ	PHE- 62	4.21	0	Hydrophobic	false
C5S	CZ	PHE- 62	4.23	0	Hydrophobic	false
CB1	CG	PHE- 67	3.66	0	Hydrophobic	false
CG1	CE1	PHE- 67	3.84	0	Hydrophobic	false
SG2	CZ	PHE- 67	4.28	0	Hydrophobic	false
SG2	CD1	LEU- 69	4.15	0	Hydrophobic	false
C2S	CD1	LEU- 69	4.07	0	Hydrophobic	false
C5S	CD1	LEU- 69	3.98	0	Hydrophobic	false
C4S	CZ	PHE- 71	4.11	0	Hydrophobic	false
C6S	CZ	PHE- 71	4.02	0	Hydrophobic	false
C4S	CD2	LEU- 92	4.2	0	Hydrophobic	false
C6S	CD1	LEU- 92	3.55	0	Hydrophobic	false
CG1	CG2	THR- 101	3.81	0	Hydrophobic	false
N1	OD1	ASN- 103	2.58	158.25	H-Bond (Ligand Donor)	false
O11	ND2	ASN- 103	2.88	169.27	H-Bond (Protein Donor)	false
O11	CZ	ARG- 122	3.63	0	Ionic (Protein Cationic)	false
C2S	SD	MET- 157	4.1	0	Hydrophobic	false
C1S	SD	MET- 157	3.64	0	Hydrophobic	false
C1S	CD2	LEU- 160	3.64	0	Hydrophobic	false
CB2	CZ	PHE- 162	3.98	0	Hydrophobic	false
C3S	CD1	LEU- 174	4.08	0	Hydrophobic	false
C5S	CE	MET- 179	3.35	0	Hydrophobic	false
C2S	CD2	LEU- 182	4.16	0	Hydrophobic	false
C5S	CD2	LEU- 182	4.2	0	Hydrophobic	false