scPDB - 4m52 entry

Protein Data Bank Entry:

PDB ID : 4m52

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-08-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrolipoyl dehydrogenase
ID:	DLDH_MYCTO
AC:	P9WHH8
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83331
EC Number:	1.8.1.4

Chains:

Chain Name:	Percentage of Residues within binding site
B	56 %
C	31 %
D	13 %

Ligand binding site composition:

B-Factor:	36.385
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.352	2281.500

% Hydrophobic	% Polar
40.68	59.32
According to VolSite

Ligand :

HET Code:	M52
Formula:	C15H17BrN4O4S
Molecular weight:	429.289 g/mol
DrugBank ID:	-
Buried Surface Area:	67.76 %
Polar Surface area:	122.99 Å2

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

Mass center Coordinates

X	Y	Z
-80.5065	18.2458	36.5154

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
BR	CB	PRO- 13	3.64	0	Hydrophobic	false
BR	CE2	TYR- 16	4.35	0	Hydrophobic	false
BR	CD1	LEU- 42	4.12	0	Hydrophobic	false
C14	CD1	LEU- 42	4.34	0	Hydrophobic	false
C09	CD2	LEU- 42	4.09	0	Hydrophobic	false
C09	CB	ARG- 93	4.43	0	Hydrophobic	false
C09	CG2	VAL- 97	3.88	0	Hydrophobic	false
C06	CZ	PHE- 99	3.81	0	Hydrophobic	false
C03	CE2	PHE- 99	3.44	0	Hydrophobic	false
C10	CD1	LEU- 100	4.41	0	Hydrophobic	false
C04	CD2	LEU- 100	4.03	0	Hydrophobic	false
BR	CB	ALA- 317	4.46	0	Hydrophobic	false
BR	CG	GLU- 321	4.39	0	Hydrophobic	false
N04	O	ALA- 381	2.84	135.58	H-Bond (Ligand Donor)	false
C04	CB	ALA- 381	4.26	0	Hydrophobic	false
C10	CB	ASN- 463	4.09	0	Hydrophobic	false
N02	O	ASN- 463	2.76	165.03	H-Bond (Ligand Donor)	false
C06	CE2	PHE- 464	4.3	0	Hydrophobic	false