scPDB - 4lj7 entry

Protein Data Bank Entry:

PDB ID : 4lj7

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2013-07-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chaperone protein ClpB
ID:	CLPB_THET8
AC:	Q9RA63
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	50.797
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.436	617.625

% Hydrophobic	% Polar
39.89	60.11
According to VolSite

Ligand :

HET Code:	MNT
Formula:	C18H19N6O10P2
Molecular weight:	541.325 g/mol
DrugBank ID:	DB03126
Buried Surface Area:	63.84 %
Polar Surface area:	258.57 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-13.1202	-16.3006	-20.6639

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
N6	O	VAL- 561	2.58	163.6	H-Bond (Ligand Donor)	false
N1	N	VAL- 561	2.68	169.68	H-Bond (Protein Donor)	false
O2B	N	GLY- 598	2.78	147.32	H-Bond (Protein Donor)	false
O1B	N	VAL- 599	2.98	126.64	H-Bond (Protein Donor)	false
N6	O	VAL- 599	3.17	139.93	H-Bond (Ligand Donor)	false
O1B	N	GLY- 600	3.09	150.55	H-Bond (Protein Donor)	false
O1B	N	GLN- 601	2.89	165.7	H-Bond (Protein Donor)	false
O3B	N	THR- 602	2.67	151.64	H-Bond (Protein Donor)	false
O3B	OG1	THR- 602	2.62	154.15	H-Bond (Protein Donor)	false
O1A	N	GLU- 603	3.19	170.86	H-Bond (Protein Donor)	false
C2B	CB	GLU- 603	3.94	0	Hydrophobic	false
C1B	CG2	ILE- 765	4.25	0	Hydrophobic	false
C5'	CG	GLN- 769	3.65	0	Hydrophobic	false
C1B	CB	ALA- 805	4.49	0	Hydrophobic	false
O2B	CZ	ARG- 806	3.21	0	Ionic (Protein Cationic)	false
O3A	NE	ARG- 806	3.29	170.2	H-Bond (Protein Donor)	false
C5B	CG	ARG- 806	3.51	0	Hydrophobic	false
C5'	CD2	LEU- 808	4.39	0	Hydrophobic	false
CM'	CD	ARG- 809	4.2	0	Hydrophobic	false
C3'	CG	ARG- 809	3.55	0	Hydrophobic	false
C6'	CB	ARG- 809	3.88	0	Hydrophobic	false
C5'	CD1	ILE- 812	4.14	0	Hydrophobic	false