scPDB - 1xpg entry

Protein Data Bank Entry:

PDB ID : 1xpg

Resolution :2.590 Å

Experimental Method : X-ray

Deposition Date : 2004-10-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
ID:	METE_THEMA
AC:	Q9X112
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	2.1.1.14

Chains:

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

Ligand binding site composition:

B-Factor:	25.383
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.867	1380.375

% Hydrophobic	% Polar
32.52	67.48
According to VolSite

Ligand :

HET Code:	C2F
Formula:	C20H23N7O6
Molecular weight:	457.440 g/mol
DrugBank ID:	-
Buried Surface Area:	46.34 %
Polar Surface area:	204.14 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
117.268	67.5301	39.3608

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
CB	CZ3	TRP- 486	4.15	0	Hydrophobic	false
C9	CB	SER- 489	4.23	0	Hydrophobic	false
C16	CB	SER- 489	3.9	0	Hydrophobic	false
C12	CB	ARG- 493	3.89	0	Hydrophobic	false
N	O	CYS- 494	3.13	135.78	H-Bond (Ligand Donor)	false
O1	O	CYS- 494	2.75	167.17	H-Bond (Ligand Donor)	false
O1	N	CYS- 494	2.66	153.94	H-Bond (Protein Donor)	false
C6	CD2	TYR- 495	4.13	0	Hydrophobic	false
C7	CE2	TYR- 495	4.34	0	Hydrophobic	false
C11	CG	TYR- 495	4.44	0	Hydrophobic	false
C16	CB	TYR- 495	4.49	0	Hydrophobic	false
C7	CZ3	TRP- 539	3.69	0	Hydrophobic	false
C11	CD2	TRP- 539	3.7	0	Hydrophobic	false
NA2	OE2	GLU- 583	3.43	141.75	H-Bond (Ligand Donor)	false
NA2	OE1	GLU- 583	3.07	157.58	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 583	3.15	158.52	H-Bond (Ligand Donor)	false