scPDB - 1cl2 entry

Protein Data Bank Entry:

PDB ID : 1cl2

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1997-09-04

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:	11.382
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.012	317.250

% Hydrophobic	% Polar
55.32	44.68
According to VolSite

Ligand :

HET Code:	PPG
Formula:	C14H18N3O8P
Molecular weight:	387.282 g/mol
DrugBank ID:	DB03287
Buried Surface Area:	59.56 %
Polar Surface area:	204.7 Å2

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

Mass center Coordinates

X	Y	Z
-9.09692	47.6803	25.8061

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
OP1	N	GLY- 86	2.78	161.19	H-Bond (Protein Donor)	false
C5A	CB	ALA- 87	4.4	0	Hydrophobic	false
OP3	N	ALA- 87	2.96	160.62	H-Bond (Protein Donor)	false
C2A	CB	TYR- 111	4.41	0	Hydrophobic	false
C5A	CE2	TYR- 111	3.51	0	Hydrophobic	false
CGI	CZ	TYR- 111	3.93	0	Hydrophobic	false
NI	OH	TYR- 111	2.67	134.63	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 111	3.84	0	Aromatic Face/Face	false
N1	OD2	ASP- 185	2.78	164.53	H-Bond (Ligand Donor)	false
C2A	CB	THR- 187	4.03	0	Hydrophobic	false
C5	CB	ALA- 207	3.86	0	Hydrophobic	false
OP1	OG1	THR- 209	2.64	126.24	H-Bond (Protein Donor)	false
OP2	NZ	LYS- 210	3.78	0	Ionic (Protein Cationic)	false
N4A	NZ	LYS- 210	3.38	138.43	H-Bond (Protein Donor)	false
CEI	CG	TYR- 338	4.36	0	Hydrophobic	false
CBI	CB	TYR- 338	4.21	0	Hydrophobic	false
O3B	N	SER- 339	2.94	159.99	H-Bond (Protein Donor)	false
CBI	CB	SER- 339	4.31	0	Hydrophobic	false
C2A	CZ2	TRP- 340	4.16	0	Hydrophobic	false
O3	NE1	TRP- 340	3.23	132.42	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 340	3.01	134.21	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 372	3.44	130.15	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 372	2.78	166.04	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 372	2.98	167.47	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 372	3.54	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 372	3.83	0	Ionic (Protein Cationic)	false