scPDB - 3rim entry

Protein Data Bank Entry:

PDB ID : 3rim

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2011-04-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Transketolase
ID:	TKT_MYCTU
AC:	P9WG25
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	19.871
Number of residues:	47
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.644	840.375

% Hydrophobic	% Polar
41.77	58.23
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	82.98 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-5.18435	-17.3946	67.7938

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
O3A	NE2	HIS- 85	2.81	169.9	H-Bond (Protein Donor)	false
N4'	O	GLY- 133	2.94	158.85	H-Bond (Ligand Donor)	false
CM2	CB	LEU- 135	4.23	0	Hydrophobic	false
C5'	CD1	LEU- 135	3.98	0	Hydrophobic	false
S1	CD1	LEU- 135	3.67	0	Hydrophobic	false
CM4	CD1	LEU- 135	4.27	0	Hydrophobic	false
C6	CD1	LEU- 135	4.07	0	Hydrophobic	false
N3'	N	LEU- 135	3.08	166.17	H-Bond (Protein Donor)	false
O1A	OG	SER- 176	2.56	174.01	H-Bond (Protein Donor)	false
O1A	N	GLY- 178	2.85	150.56	H-Bond (Protein Donor)	false
CM2	CG	GLU- 182	4.29	0	Hydrophobic	false
O2B	ND2	ASN- 207	2.82	150.62	H-Bond (Protein Donor)	false
C7	CB	SER- 210	3.98	0	Hydrophobic	false
S1	CD1	ILE- 211	4.23	0	Hydrophobic	false
CM4	CD1	ILE- 211	4.11	0	Hydrophobic	false
C6	CG1	ILE- 211	4.1	0	Hydrophobic	false
CM4	CB	ASP- 401	4.18	0	Hydrophobic	false
CM4	CD2	LEU- 402	3.75	0	Hydrophobic	false
CM4	CG2	VAL- 439	3.78	0	Hydrophobic	false
C6	CG2	VAL- 439	4.3	0	Hydrophobic	false
CM2	CD1	PHE- 467	3.95	0	Hydrophobic	false
DuAr	DuAr	PHE- 467	3.69	0	Aromatic Face/Face	false
CM2	CZ	TYR- 470	3.42	0	Hydrophobic	false
O2A	MG	MG- 1001	1.95	0	Metal Acceptor	false
O2B	MG	MG- 1001	2.46	0	Metal Acceptor	false