scPDB - 2gqn entry

Protein Data Bank Entry:

PDB ID : 2gqn

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2006-04-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cystathionine beta-lyase MetC
ID:	METC_ECOLI
AC:	P06721
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.4.1.8

Chains:

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

Ligand binding site composition:

B-Factor:	15.738
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.517	523.125

% Hydrophobic	% Polar
56.13	43.87
According to VolSite

Ligand :

HET Code:	BLP
Formula:	C17H18N5O9P
Molecular weight:	467.327 g/mol
DrugBank ID:	-
Buried Surface Area:	55.2 %
Polar Surface area:	231.39 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-9.90784	48.1588	26.2968

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
O3	N	GLY- 86	2.88	163.32	H-Bond (Protein Donor)	false
C5	CB	ALA- 87	4.42	0	Hydrophobic	false
O4	N	ALA- 87	2.8	168.32	H-Bond (Protein Donor)	false
C17	CB	TYR- 111	4.48	0	Hydrophobic	false
C1	CB	TYR- 111	4.28	0	Hydrophobic	false
C5	CE2	TYR- 111	3.36	0	Hydrophobic	false
DuAr	DuAr	TYR- 111	3.69	0	Aromatic Face/Face	false
C15	CG	PRO- 113	4.15	0	Hydrophobic	false
N1	OD2	ASP- 185	2.63	160.13	H-Bond (Ligand Donor)	false
C1	CB	THR- 187	4.22	0	Hydrophobic	false
C4	CB	ALA- 207	3.83	0	Hydrophobic	false
O3	OG1	THR- 209	2.68	169.48	H-Bond (Protein Donor)	false
N2	NZ	LYS- 210	2.91	137.98	H-Bond (Protein Donor)	false
O2	NZ	LYS- 210	3.49	0	Ionic (Protein Cationic)	false
O9	NE1	TRP- 340	2.98	140.9	H-Bond (Protein Donor)	false
C1	CZ2	TRP- 340	3.95	0	Hydrophobic	false
O5	NH2	ARG- 372	3.32	151.96	H-Bond (Protein Donor)	false
O5	NH1	ARG- 372	3.44	145.42	H-Bond (Protein Donor)	false