scPDB - 2c2b entry

Protein Data Bank Entry:

PDB ID : 2c2b

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2005-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Threonine synthase 1, chloroplastic
ID:	THRC1_ARATH
AC:	Q9S7B5
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	4.2.3.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	57.450
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.655	573.750

% Hydrophobic	% Polar
44.12	55.88
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	70.23 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
43.8156	34.2514	71.5735

Binding mode :

What is Poseview ?

2D View
3D View

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
CG	CB	SER- 99	4.5	0	Hydrophobic	false
C5'	CB	SER- 99	3.91	0	Hydrophobic	false
N6	O	PRO- 102	3.07	155.5	H-Bond (Ligand Donor)	false
N1	N	GLY- 104	3.05	135.02	H-Bond (Protein Donor)	false
N6	OG	SER- 125	3.12	153.93	H-Bond (Ligand Donor)	false
C2'	CD1	PHE- 127	4.03	0	Hydrophobic	false
CE	CD2	LEU- 133	3.7	0	Hydrophobic	false
C4'	CB	LEU- 133	4.3	0	Hydrophobic	false
C2'	CB	LEU- 133	4.46	0	Hydrophobic	false
O2'	N	LEU- 133	2.78	170.27	H-Bond (Protein Donor)	false
CB	CH2	TRP- 150	4.27	0	Hydrophobic	false
SD	CH2	TRP- 150	3.51	0	Hydrophobic	false
CE	CZ3	TRP- 150	3.49	0	Hydrophobic	false
CE	CE1	PHE- 282	3.68	0	Hydrophobic	false
CB	CD1	PHE- 282	4.02	0	Hydrophobic	false