scPDB - 3i59 entry

Protein Data Bank Entry:

PDB ID : 3i59

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2009-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CRP-like cAMP-activated global transcriptional regulator
ID:	CRPL_MYCTU
AC:	P9WMH3
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
B	11 %

Ligand binding site composition:

B-Factor:	58.476
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.408	1157.625

% Hydrophobic	% Polar
49.27	50.73
According to VolSite

Ligand :

HET Code:	N6R
Formula:	C19H21N5O6P
Molecular weight:	446.374 g/mol
DrugBank ID:	-
Buried Surface Area:	68.27 %
Polar Surface area:	153.49 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-1.61974	18.6159	-22.8448

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
C5S	CE1	PHE- 38	3.37	0	Hydrophobic	false
C1S	CG2	ILE- 57	3.91	0	Hydrophobic	false
C4S	CG2	ILE- 57	4.47	0	Hydrophobic	false
C5H	CB	LEU- 69	3.64	0	Hydrophobic	false
C5U	CD2	LEU- 69	3.91	0	Hydrophobic	false
C5M	CD1	LEU- 69	3.61	0	Hydrophobic	false
C1S	CE	MET- 72	4.4	0	Hydrophobic	false
O2S	N	GLY- 79	2.98	140.65	H-Bond (Protein Donor)	false
O2S	OE1	GLU- 80	2.79	129.68	H-Bond (Ligand Donor)	false
O2S	OE2	GLU- 80	2.86	156.46	H-Bond (Ligand Donor)	false
O3S	N	LEU- 81	3.43	141.72	H-Bond (Protein Donor)	false
C2S	CG	LEU- 81	3.91	0	Hydrophobic	false
O5B	N	SER- 82	3.21	166.39	H-Bond (Protein Donor)	false
O5B	OG	SER- 82	2.61	142.58	H-Bond (Ligand Donor)	false
O5B	NH2	ARG- 89	3.12	159.12	H-Bond (Protein Donor)	false
O5D	OG1	THR- 90	2.64	161.51	H-Bond (Protein Donor)	false
O5D	N	THR- 90	2.79	165.57	H-Bond (Protein Donor)	false
O4S	OG	SER- 91	3.32	124.59	H-Bond (Protein Donor)	false
C5S	CB	SER- 91	4.38	0	Hydrophobic	false
C5Y	CB	THR- 134	4.48	0	Hydrophobic	false
C5A	CG2	THR- 134	3.46	0	Hydrophobic	false
C5A	CG2	THR- 134	4.06	0	Hydrophobic	false
N7	ND2	ASN- 135	2.76	130.77	H-Bond (Protein Donor)	false
C5F	CB	ASN- 137	3.55	0	Hydrophobic	false
C5E	CB	ASN- 137	3.27	0	Hydrophobic	false
C5I	CD1	LEU- 138	4.27	0	Hydrophobic	false
C5G	CD1	LEU- 141	3.39	0	Hydrophobic	false