scPDB - 1tkb entry

Protein Data Bank Entry:

PDB ID : 1tkb

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1994-02-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Transketolase 1
ID:	TKT1_YEAST
AC:	P23254
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.2.1.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	72 %
B	28 %

Ligand binding site composition:

B-Factor:	13.218
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.716	826.875

% Hydrophobic	% Polar
43.27	56.73
According to VolSite

Ligand :

HET Code:	N1T
Formula:	C13H17N3O7P2S
Molecular weight:	421.303 g/mol
DrugBank ID:	DB01658
Buried Surface Area:	78.86 %
Polar Surface area:	212.42 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-4.59938	57.546	15.3202

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
O3B	NE2	HIS- 69	2.79	160.22	H-Bond (Protein Donor)	false
N4'	O	GLY- 116	2.93	171.77	H-Bond (Ligand Donor)	false
CM2	CB	LEU- 118	4.05	0	Hydrophobic	false
C5'	CD1	LEU- 118	4.32	0	Hydrophobic	false
S1	CD1	LEU- 118	3.93	0	Hydrophobic	false
CM4	CD1	LEU- 118	4.26	0	Hydrophobic	false
C6	CD1	LEU- 118	3.9	0	Hydrophobic	false
N3'	N	LEU- 118	3.08	154.43	H-Bond (Protein Donor)	false
O2A	N	ASP- 157	3.33	148.05	H-Bond (Protein Donor)	false
O1A	N	GLY- 158	3.27	144.77	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 187	3.05	131.9	H-Bond (Protein Donor)	false
C7	CB	THR- 190	3.85	0	Hydrophobic	false
S1	CD1	ILE- 191	4.17	0	Hydrophobic	false
CM4	CD1	ILE- 191	3.82	0	Hydrophobic	false
C7	CG1	ILE- 191	3.78	0	Hydrophobic	false
O2B	ND1	HIS- 263	2.6	126.18	H-Bond (Protein Donor)	false
O3B	ND1	HIS- 263	3.49	147.33	H-Bond (Protein Donor)	false
CM4	CB	ASP- 382	4.03	0	Hydrophobic	false
C6'	CD1	LEU- 383	4.4	0	Hydrophobic	false
CM4	CG	LEU- 383	4.43	0	Hydrophobic	false
C1'	CG2	ILE- 416	4.4	0	Hydrophobic	false
CM4	CG1	ILE- 416	3.58	0	Hydrophobic	false
C6	CD1	ILE- 416	3.81	0	Hydrophobic	false
C1'	CB	PHE- 445	4.38	0	Hydrophobic	false
CM2	CD1	PHE- 445	3.94	0	Hydrophobic	false
CM2	CZ	TYR- 448	3.52	0	Hydrophobic	false
O2A	CA	CA- 682	2.2	0	Metal Acceptor	false