scPDB - 2clm entry

Protein Data Bank Entry:

PDB ID : 2clm

Resolution :1.510 Å

Experimental Method : X-ray

Deposition Date : 2006-04-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan synthase alpha chain
ID:	TRPA_SALTY
AC:	P00929
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	88 %
B	12 %

Ligand binding site composition:

B-Factor:	24.484
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.677	334.125

% Hydrophobic	% Polar
52.53	47.47
According to VolSite

Ligand :

HET Code:	F6F
Formula:	C10H9F3NO6P
Molecular weight:	327.151 g/mol
DrugBank ID:	DB07745
Buried Surface Area:	67.38 %
Polar Surface area:	120.56 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
49.9501	25.9298	13.3029

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
F10	CB	PRO- 18	3.25	0	Hydrophobic	false
C6	CB	ALA- 59	4.16	0	Hydrophobic	false
F10	CB	ALA- 59	3.5	0	Hydrophobic	false
C16	CD1	ILE- 64	3.47	0	Hydrophobic	false
C5	CG	LEU- 100	4.21	0	Hydrophobic	false
C2	CD2	LEU- 100	3.74	0	Hydrophobic	false
C2	CD1	LEU- 127	4.08	0	Hydrophobic	false
C1	CB	ALA- 129	4.16	0	Hydrophobic	false
F10	CB	ALA- 129	4.06	0	Hydrophobic	false
F9	CG1	ILE- 153	4.13	0	Hydrophobic	false
C2	CD1	ILE- 153	3.88	0	Hydrophobic	false
C8	CD1	ILE- 153	3.67	0	Hydrophobic	false
O14	OH	TYR- 175	2.79	149.05	H-Bond (Protein Donor)	false
O20	N	PHE- 212	3.13	126.56	H-Bond (Protein Donor)	false
F11	CZ	PHE- 212	3.4	0	Hydrophobic	false
O21	N	GLY- 213	3.13	173.96	H-Bond (Protein Donor)	false
O19	N	GLY- 234	3.04	164.82	H-Bond (Protein Donor)	false
O17	N	SER- 235	3	155.45	H-Bond (Protein Donor)	false
O17	OG	SER- 235	2.98	164.24	H-Bond (Protein Donor)	false
O19	N	SER- 235	3.43	139.19	H-Bond (Protein Donor)	false
O19	O	HOH- 2180	2.73	156.22	H-Bond (Protein Donor)	false
O19	O	HOH- 2201	2.66	179.97	H-Bond (Protein Donor)	false