scPDB - 2isj entry

Protein Data Bank Entry:

PDB ID : 2isj

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-10-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,6-dimethylbenzimidazole synthase
ID:	BLUB_RHIME
AC:	Q92PC8
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	1.13.11.79

Chains:

Chain Name:	Percentage of Residues within binding site
G	40 %
H	60 %

Ligand binding site composition:

B-Factor:	27.769
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.020	334.125

% Hydrophobic	% Polar
43.43	56.57
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	81.1 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
75.1216	38.2551	52.8406

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
O2P	NH1	ARG- 30	2.71	145.34	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 30	3.3	124.79	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 30	2.71	136.37	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 30	3.41	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 30	3.7	0	Ionic (Protein Cationic)	false
O1P	NE	ARG- 31	2.72	157.33	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 31	3.32	128.73	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 31	2.74	159	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 31	3.44	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 31	3.66	0	Ionic (Protein Cationic)	false
C1'	CB	ASP- 32	3.71	0	Hydrophobic	false
C3'	CB	ASP- 32	4.09	0	Hydrophobic	false
O2P	N	ASP- 32	2.67	123.45	H-Bond (Protein Donor)	false
N1	NH2	ARG- 34	3.23	160.39	H-Bond (Protein Donor)	false
O2	NE	ARG- 34	2.72	153.05	H-Bond (Protein Donor)	false
O2	NH2	ARG- 34	3.4	125.91	H-Bond (Protein Donor)	false
C8M	CG	PRO- 58	4.1	0	Hydrophobic	false
O3'	N	SER- 59	3.3	136.08	H-Bond (Protein Donor)	false
C7	CB	VAL- 60	3.85	0	Hydrophobic	false
C8	CB	VAL- 60	4.15	0	Hydrophobic	false
C4'	CB	PHE- 62	3.95	0	Hydrophobic	false
C5'	CD1	PHE- 62	3.79	0	Hydrophobic	false
N3	O	LEU- 108	2.88	134.34	H-Bond (Ligand Donor)	false
C7M	SD	MET- 140	3.41	0	Hydrophobic	false
C7M	CB	TYR- 143	3.88	0	Hydrophobic	false
C8M	CB	SER- 144	4.01	0	Hydrophobic	false
C6	CB	TRP- 165	4.41	0	Hydrophobic	false
C7M	CZ2	TRP- 165	3.69	0	Hydrophobic	false
C8M	CE3	TRP- 165	4.49	0	Hydrophobic	false
C9A	CB	TRP- 165	4.11	0	Hydrophobic	false
O4	N	SER- 167	2.91	168.15	H-Bond (Protein Donor)	false
C6	CB	SER- 167	4.28	0	Hydrophobic	false
C5'	CB	PRO- 202	3.56	0	Hydrophobic	false
O4'	O	HOH- 778	2.62	156.19	H-Bond (Protein Donor)	false