scPDB - 2r8o entry

Protein Data Bank Entry:

PDB ID : 2r8o

Resolution :1.470 Å

Experimental Method : X-ray

Deposition Date : 2007-09-11

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_ECOLI
AC:	P27302
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	65 %
B	35 %

Ligand binding site composition:

B-Factor:	5.632
Number of residues:	59
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.078	526.500

% Hydrophobic	% Polar
37.18	62.82
According to VolSite

Ligand :

HET Code:	T5X
Formula:	C17H25N4O15P3S
Molecular weight:	650.384 g/mol
DrugBank ID:	-
Buried Surface Area:	76.08 %
Polar Surface area:	388.47 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
12.4424	-15.4842	9.18217

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
OX3	NE2	HIS- 26	3.03	156.83	H-Bond (Ligand Donor)	false
O3B	NE2	HIS- 66	2.79	171.8	H-Bond (Protein Donor)	false
CX1	CB	HIS- 66	3.56	0	Hydrophobic	false
OX1	NE2	HIS- 100	2.83	168.89	H-Bond (Ligand Donor)	false
N4,	O	GLY- 114	2.8	178.46	H-Bond (Ligand Donor)	false
S1	CD1	LEU- 116	4.32	0	Hydrophobic	false
CM4	CD1	LEU- 116	4.17	0	Hydrophobic	false
C5,	CD1	LEU- 116	3.77	0	Hydrophobic	false
CM2	CB	LEU- 116	4	0	Hydrophobic	false
C7	CD1	LEU- 116	3.99	0	Hydrophobic	false
N3,	N	LEU- 116	3.18	176.9	H-Bond (Protein Donor)	false
O1A	N	ASP- 155	3.35	124.15	H-Bond (Protein Donor)	false
O2A	N	GLY- 156	2.91	150.22	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 185	2.89	159.6	H-Bond (Protein Donor)	false
C6	CG1	ILE- 189	3.82	0	Hydrophobic	false
S1	CD1	ILE- 189	3.98	0	Hydrophobic	false
CX3	CD1	ILE- 189	3.76	0	Hydrophobic	false
CM4	CD1	ILE- 189	3.88	0	Hydrophobic	false
OX3	NE2	HIS- 261	2.8	161.6	H-Bond (Protein Donor)	false
CM4	CB	ASP- 381	4	0	Hydrophobic	false
CM4	CD2	LEU- 382	4.09	0	Hydrophobic	false
OX7	OG	SER- 385	2.6	161.56	H-Bond (Protein Donor)	false
CM4	CG2	VAL- 409	4	0	Hydrophobic	false
N1,	OE2	GLU- 411	2.67	167.32	H-Bond (Ligand Donor)	false
CX5	CZ	PHE- 434	3.7	0	Hydrophobic	false
CX4	CE2	PHE- 434	3.75	0	Hydrophobic	false
CM2	CD1	PHE- 437	3.8	0	Hydrophobic	false
DuAr	DuAr	PHE- 437	3.72	0	Aromatic Face/Face	false
CM2	CZ	TYR- 440	3.31	0	Hydrophobic	false
OX6	NE2	HIS- 461	2.8	148.81	H-Bond (Protein Donor)	false
OX4	OD2	ASP- 469	2.63	152.96	H-Bond (Ligand Donor)	false
OX2	NE2	HIS- 473	2.66	126.3	H-Bond (Ligand Donor)	false
OX6	NH2	ARG- 520	3.31	123.7	H-Bond (Protein Donor)	false
OX6	NE	ARG- 520	2.82	136.9	H-Bond (Protein Donor)	false
OX6	CZ	ARG- 520	3.44	0	Ionic (Protein Cationic)	false
O1A	CA	CA- 670	2.21	0	Metal Acceptor	false
O2B	CA	CA- 670	2.27	0	Metal Acceptor	false
O3B	O	HOH- 737	3.12	132.54	H-Bond (Protein Donor)	false
O3B	O	HOH- 793	3.04	162.02	H-Bond (Protein Donor)	false