scPDB - 4itx entry

Protein Data Bank Entry:

PDB ID : 4itx

Resolution :1.610 Å

Experimental Method : X-ray

Deposition Date : 2013-01-19

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:	11.146
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.225	499.500

% Hydrophobic	% Polar
54.73	45.27
According to VolSite

Ligand :

HET Code:	IN5
Formula:	C10H15N2O8P2
Molecular weight:	353.182 g/mol
DrugBank ID:	DB03327
Buried Surface Area:	66.98 %
Polar Surface area:	204.96 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-8.08564	47.5968	24.9707

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
O5	N	GLY- 86	2.8	161.84	H-Bond (Protein Donor)	false
C7	CB	ALA- 87	4.2	0	Hydrophobic	false
O3	N	ALA- 87	2.87	159.36	H-Bond (Protein Donor)	false
C3	CB	TYR- 111	4.17	0	Hydrophobic	false
C7	CE2	TYR- 111	3.52	0	Hydrophobic	false
C10	CZ	TYR- 111	4.07	0	Hydrophobic	false
C6	CB	TYR- 111	4.32	0	Hydrophobic	false
DuAr	DuAr	TYR- 111	3.99	0	Aromatic Face/Face	false
N1	OD2	ASP- 185	2.57	163.39	H-Bond (Ligand Donor)	false
C6	CB	THR- 187	4.06	0	Hydrophobic	false
C5	CB	ALA- 207	3.9	0	Hydrophobic	false
O5	OG1	THR- 209	2.6	125.14	H-Bond (Protein Donor)	false
O4	NZ	LYS- 210	3.42	0	Ionic (Protein Cationic)	false
C10	CB	TYR- 338	4.32	0	Hydrophobic	false
C10	CB	SER- 339	4.49	0	Hydrophobic	false
O6	N	SER- 339	2.63	153.03	H-Bond (Protein Donor)	false
C6	CZ2	TRP- 340	4.19	0	Hydrophobic	false
O8	NE1	TRP- 340	2.98	146.63	H-Bond (Protein Donor)	false
O6	NH2	ARG- 372	2.83	167.67	H-Bond (Protein Donor)	false
O8	NH2	ARG- 372	3.3	126.5	H-Bond (Protein Donor)	false
O8	NH1	ARG- 372	2.61	158.1	H-Bond (Protein Donor)	false
O6	CZ	ARG- 372	3.77	0	Ionic (Protein Cationic)	false
O8	CZ	ARG- 372	3.38	0	Ionic (Protein Cationic)	false