scPDB - 2gej entry

Protein Data Bank Entry:

PDB ID : 2gej

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2006-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphatidyl-myo-inositol mannosyltransferase
ID:	PIMA_MYCS2
AC:	A0QWG6
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	2.4.1.57

Chains:

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

Ligand binding site composition:

B-Factor:	46.602
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.145	1238.625

% Hydrophobic	% Polar
47.68	52.32
According to VolSite

Ligand :

HET Code:	GDD
Formula:	C16H23N5O16P2
Molecular weight:	603.325 g/mol
DrugBank ID:	-
Buried Surface Area:	63.49 %
Polar Surface area:	352.71 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	8
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-1.85451	44.4433	28.7011

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
O3B	N	GLY- 16	2.77	161.71	H-Bond (Protein Donor)	false
C21	CG2	THR- 119	4.27	0	Hydrophobic	false
O2B	CZ	ARG- 196	3.16	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 202	3.4	148.68	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 202	2.7	154.23	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 202	3.4	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 202	2.7	0	Ionic (Protein Cationic)	false
N2	O	VAL- 251	2.71	146.48	H-Bond (Ligand Donor)	false
N1	O	VAL- 251	2.72	143.66	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 253	2.67	165.19	H-Bond (Ligand Donor)	false
N3	NZ	LYS- 256	3.18	147.8	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 256	3.09	135.6	H-Bond (Protein Donor)	false
O41	OE1	GLU- 274	2.52	129.63	H-Bond (Protein Donor)	false
O31	N	SER- 275	2.84	163.25	H-Bond (Protein Donor)	false
C41	CB	PHE- 276	4.33	0	Hydrophobic	false
O41	N	PHE- 276	3.06	147.86	H-Bond (Protein Donor)	false
C61	CG2	ILE- 278	3.59	0	Hydrophobic	false
C3'	CG2	ILE- 278	3.7	0	Hydrophobic	false
O6A	N	ILE- 278	3.05	154.97	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 279	4.02	0	Hydrophobic	false
O2'	OE2	GLU- 282	2.91	123.13	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 282	2.68	151.79	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 282	2.64	164.83	H-Bond (Ligand Donor)	false
O3B	O	HOH- 2575	3.45	179.98	H-Bond (Protein Donor)	false